Jamis Dragon
I built this bike back in 2003 for the Great Divide Mountain Bike Route. I made a few changes before this trip, and it held up remarkably well. Some key features:
  • Front suspension. I almost went with a rigid fork, but decided on a Magura Odur Tour at the last minute. On the dirt roads, I'm sure I was more comfortable for it, and it only had to be oiled twice during the trip. It also only weighed one pound more than my rigid fork, so overall it was a no-brainer.
  • Drop handlebars. I went with drops for two reasons - more hand positions and the ability to use bar-end shifters. It was great being able to duck out of the headwinds, and I liked the simplicity of non-indexed bar-end shifters over rapid fires. Unfortunately even bar-end shifters can have problems - mine became corroded in Central America making them very hard to move and I had trouble finding replacements on the road. After replacing the bad shifter in Colombia, I carried a spare for the rest of my trip, which I never ended up needing.
  • Steel Frame. Steel is generally recommended for a few reasons - it gives a more comfortable ride, it bends before breaking (unlike aluminum) and can be welded easily if it does break. My frame was made with the well-regarded Reynolds 853 steel for the main triangle. 
  • Suspension seatpost. I got this for the Divide and was amazed that it held up for as long as it did. Even the elastomers never dried up or cracked. I used a Cane Creek Thudbuster, which adds a little weight, but for the comfort it's totally worth it. (A sprung Brooks saddle is another appealing option).
  • Disc brakes. I love Avid BB7s. I used BB7s on the Divide and for the PanAm. I never had to change a rotor, but occasionally had to slightly bend them back into true. The calipers are very easy to adjust, the brake pads last a long time, and more importantly, unlike rim brakes, you're not wearing out your rim every time you stop - it happens. Friends with hydraulic discs had a problem with overheating on long descents. In the Andes, you can have descents that last for hours - good brakes are critical. 
  • Tires. Schwalbe Marathon XRs have since been replaced by a newer model, but if they're anywhere near as good as the XRs, I have to recommend them. I was skeptical when I heard people had done the whole route on two pairs of tires, but it's definitely possible. I started with 1.6 or 1.7 inch tires, and changed to 2.1s in Mexico. I had to replace my rear tire a few weeks before swapping with 2.1s, and my rear 2.1 lasted until just north of San Martin de Los Andes in Argentina. 
  • Tubes. I had only two flat tires from the coast of Mexico to Ushuaia in Argentina. Both were the rear tire and within a few days of each other. My front tire didn't have a single flat from the time I changed it in Mexico, to when I finished in Ushuaia. How could I not recommend Slime Lite tubes?!
  • Saddles. I used a total of four saddles on this trip. I was very happy with an anatomical saddle made by Serfas, and another that is patented by Velo, but sold by other brands. I was uncomfortable every day on an expensive leather saddle that I started with.
  • Chains. I'm a big fan of SRAM 971 chains. Powerlinks are awesome.
  • Other components. My deraileurs, crankset and cassettes were all Shimano Deore. Middle of the line is the best for this kind of trip, and Shimano components are available everywhere.
  • Wheels. I had my wheels custom built and was amazed by how well they did - I never had a broken spoke, or a cracked rim. The rims were Rhyno Lites, which I also used on the Divide. I had DT Swiss spokes, and Phil Wood hubs. My rear hub didn't survive the trip and I had to replace it with a Shimano in Southern Chile. I don't know if I can claim that Phil Wood hubs are worth the price. I chose the hubs for the same reason I went with disc brakes - I don't think it makes sense to have to rebuild the wheel because of any part that is going to wear out. Phil Woods use sealed bearings which are relatively easy to change on the road, but note that you cannot (easily) change the freehub body bearings in the field. 
Bob Ibex
I used a BOB Ibex trailer for the entire trip, and it was always the first thing people asked about. Compared to panniers, I think there are a few main points:

The Good
  • Aerodynamics. I once read that in otherwise perfect conditions, the largest force a cyclist has to overcome is air resistance. If you use front panniers you effectively have a "wall" in front of your bike that you're pushing through the air (or into the wind). The trailer is narrower and presents a smaller surface area to the wind. 
  • Efficiency. In road cycling there is a concept known as "tire drop". The theory is that if you over-inflate your tires, you bounce up and down a little over each bump in the road, redirecting your forward momentum and deceasing your efficiency. In my mind, the same applies to carrying gear. If you're traveling on dirt roads with panniers, each bump is "lifting" the combined weight of you, your bike and your gear. When your gear is suspended in a trailer, the spring absorbs the shock and your momentum continues to travel forward. Suspension should also help protect spokes and rims from damage.
  • Durability. There are a few main points here: A trailer is less likely to break in a crash (on a trip this long, there will be crashes), the parts of a trailer that might break are easy to carry (yes, with panniers, you can carry a few metal rods and two component glue to temporarily fix some problems), and lastly, with a trailer the weight of your gear is supported by the trailer itself, not by the bag containing your gear. 
The Bad
  • Weight. In the mountains, nothing affects you as much as the weight you carry. A trailer and bag weigh more than a set of panniers and racks. So, the question is, in the long run, do the aerodynamics and suspension make up for the weight?
  • Maneuverability. There are times when the length of a trailer can cause problems - for example in crowds or trying to get onto a sidewalk. When staying in a hotel - a trailer can add an extra trip. 
  • Flats. Every cyclists least favorite thing. An extra wheel means you're at least 50% more likely to have a flat. In my case, much more. I used Schwalbe tires and slime tubes, yet consistently had more flats than on my bicycle - but still not an unacceptable number overall. (On the bright side, 16" tires and tubes are easily obtainable all through the Americas since they are used on children's bikes, and it's very easy to change a flat on the trailer.
Trailer Myths, Busted.
  • A trailer "pulls you backwards" on climbs. Physics says no - weight "pulls" you backwards, how you carry it does not. Here's a quick thought experiment: You're cycling uphill with your trailer "pulling you backwards". You have a strong string tied to the back of your trailer and to your strongest finger. You lift the trailer up as you're riding so that it's no longer touching the ground (kind of how panniers work). Did it suddenly get easier to pedal? (Answer: nope!).
  • Keeps weight off your bike. Lets compare this to a set of Ortliebs, which have a front capacity of about 20 liters and a rear capacity of about 40, and you'll put at least 20 liters of stuff on top of the rear rack. Let's say that each liter of volume contains a half pound of weight, so you have 10 pounds up front, and 30 pounds in back. If you have all the same stuff in a trailer, you still have 80 liters, or 40 pounds of stuff, divided over the axle of the trailer and the rear axle of the bike - 20 pounds on each axle. Add about 7 pounds for the tongue weight of the trailer itself and you have 27 pounds on the back of the bike - within 3 pounds of the panniers. So it doesn't make a difference as far as weight distribution goes.
  • Can unhitch easily for trips to town. Sure, but in reality it's pretty rare to leave your stuff behind, and unclipping panniers doesn't take long either. On the other hand, getting my stuff onto and off of boats was easier with the trailer than for other people with panniers, who had to remove them all before boarding.
A few more things...
Get a spare long bolt for the fork. Carry spare bearings and get them from Phil Wood. Get rid of the standard bearings as soon as possible. Get some spare spokes made before you set out. Carry a spare skewer - if you're not careful and one bends, you'll need a backup. Schwalbe makes a 16" tire that fits. 16" tires and tubes are available all through Latin America, but the pressure ratings are generally low (<=35psi) - the Schalbe threadcount is much higher and you can use much higher pressures. A spare tire fits perfectly under the trailer, attached with a few cable ties to the grill. Carry spare pins and the rubber retainers.
REI Quarterdome UL
Exped Auriga Mesh
I bought a REI Quarterdome UL shortly after it was released (2004?), and it would have been hard to convince me that a better tent existed. It was light, stable, roomy enough for me and my gear, was a good color, had two doors and vestibules and packed up small. At the end of a short trip to Utah, I pitched it under a tree that was dripping sap all night and had no choice but to say goodbye to my great tent. Before the PanAm trip in 2009 I saw that REI was still offering the same model, but only through their outlet store, and at half the price I had paid the first time - so I bought two! Unfortunately the floor started leaking after only a few weeks, and the zippers started failing shortly after. As they say, you get what you pay for. Before I had found the new Quarterdomes, I had bought an Exped Auriga Mesh online for half price, which I planned to use for the PanAm. It was almost my perfect tent, having the same qualities as the Quarterdome but with four-season materials. Unfortunately it was what I considered to be on the "heavy" side and I opted for the new Quarterdome instead. After the Quarterdome failed, I had my Dad bring my Exped with him to California, and it lasted me until the end of the trip - where I sold it for 25% of what I paid!

Key points for a tent:
  • Dull color
  • Reasonably light - it's worth some extra weight for durability though
  • No complex poles
  • I prefer a fly-first or storm-pitch tent
  • Two doors and vestibules mean the zippers last twice as long (compared to a one-door tent)
  • Freestanding tents give you a lot more pitching options
MSR Whisperlite International
You can't kill this stove. Mine was about 10 years old when I finished the PanAm and it was still going strong. You can repair almost anything that goes wrong while you're on the road if you carry the service kit. Some people seem to have problems with soot clogging the jet, but in at least one case, the person's shaker needle had been lost, which would explain it. Also, I don't think any gasoline stove is immune to soot buildup.

I think MSR could do a lot better with the pumps, which are made from brittle plastic. Supposedly plastic is used for weight savings, but I'd rather carry extra weight than eat a cold dinner (or nothing at all). I had better luck when I carried my pump and tank separately (pump in a bag, tank in a bottle cage). I always had two pumps throughout the trip. Make sure you clean the one-way valve on the pump once in a while. Also, if you roll the wind screen and gently flatten it, it will last longer than if you fold it. The heat reflector can be useful when cooking on a surface that could be damaged by heat. 

One 21 ounce fuel tank was always enough - if in doubt, just fill a Coke bottle with gas. If a gas station won't fill a Coke bottle, have them fill the tank, pour it into the bottle while you're standing there, and have them fill the tank again!

My cooking supplies were a small Open Country pot, a titanium pan that was replaced with a standard non-stick, an MSR cooking utensil kit, and a flexible cutting board.
Hydration and Purification
I carried four Camelbak Podium water bottles, two 6 liter MSR dromedary water bags, and an MSR gravity water filter. I usually filled 3-4 bottles in the morning, which was enough to get through the day. I only really needed one of the 6 liter bags. The times I used both were for balance (3 liters in each), or one to carry dirty water that I planned to filter later. I think two 3 liter bags and a couple Coke bottles when extra capacity is needed would be a safe solution.

Gravity filters are great. Just fill up the "dirty" reservoir, hang it from a tree or your bike, pitch your tent, and you have 4 or so liters of clean water waiting for you. I also used a small bottle of chlorine bleach, which I used instead of filtering if the water looked clear but when there may have been animals in the area. 
First Aid I took a Wilderness First Aid course before I left, and asked the instructor about my store-bought kit. She pointed out that it was incomplete and most of the items had expired. You're better off buying your own little bag, then going to a pharmacy and filling it with adequate quantities of whatever you think you'll need. My home made kit included:
  • Adhesive strips / plasters in many shapes and sizes
  • Ibuprofen
  • Acetaminophen
  • Alcohol wipes and sponges
  • Triple antibiotic ointment
  • Anti-diarrheals
  • Something for stomach relief
  • Second skin for blisters (never needed it myself)
  • Antibiotics (know when to take them)
  • Doxycycline, but taking Malarone after Malaria symptoms start seems more common
  • Compact wilderness first aid book
  • Medical tape
  • Compression bandage
  • Needle and thread
  • A few safety pins
SleepingI used a Thermarest 3/4 air mattress for the entire trip, with a Thermarest Z-Seat for sitting and for under my feet on cold nights. I had an EMS Mountain Light 20 degree sleeping bag, which worked well until about freezing. I tried a number of blankets, both alone and with my sleeping bag with various degrees of success. In Santiago Chile, after a number of 10 degree (F) nights, I bought a 10 degree bag, and never had another night below freezing after... I think the best combination is a compact down sleeping bag that you can use with layers of clothes and a down jacket on the really cold nights.
Organization I used a bunch of Eagle Creek products to keep my stuff organized - from clothes to tools to electronics. I highly recommend them. I also had a small Outdoor Gear duffel for my food.
Backpack I made some mistakes in this department. I started with an REI compressible daypack, sent that home when I got a larger hiking day pack, traded that for a 50 liter backpack, and eventually got my REI bag back in a care package. I recommend a backpack of at least 50 liters (preferably a little larger) for hiking and side trips by bus or plane, and a small lightweight backpack for walking around a city or day hikes.
Fanny pack and bar bag For me, both of these were indispensable. I'd always wear a fanny pack with my small camera, money and travel documents, and I could easily unclip my handlebar bag with my SLR maps and iPod, etc. when I went into a restaurant, or left my bike.
ClothesTwo pairs of convertible pants, three short sleeve shirts, three long sleeve shirts, wind-blocking fleece, rain jacket, rain pants, compressible down jacket, leg warmers, fleece shoe covers. Gloves are tricky; in the end I had gloves for rain, cold and very cold conditions. I'd like to find a good all-purpose or layered glove.
FootwearDuring the two-and-a-half years, I had plenty of time to experiment with footwear. In the end, I decided the perfect solution is a pair of breathable/waterproof hiking boots for riding and hiking, and closed sandals such as the Salomon Epic Cabrio or Keen McKenzie (or "water shoes" such as the Keen Turia or Salomon Techamphibian). I found clip-less shoes unnecessary and most long-distance tourists don't use them.
Other Stuff Tools, spare parts, maps, shaving kit. Tools and spare parts included:
  • Spare BOB skewer and long bolt for the front fork
  • Spare tire for bike and trailer
  • One spare tube for bike and trailer
  • Patch kit
  • Spokes for bike and trailer
  • Brake and shifter cable and housing (and housing cutter)
  • Hypercracker for removing the cassette - essential!
  • Topeak Alien and Leatherman
  • Assortment of allen keys for sizes not on the Alien
  • Topeak Mountain Morph pump with gauge - great pump!
  • Spare rear/right bar-end shifter
  • Spare rear derailleur
  • Fiber fix spoke
  • Grease
  • Adjustable wrench
  • Cone wrenches for trailer
  • Spare chain
  • Spare rotor
  • Spare disc brake pads
Sent home or abandonedSome things didn't make it to the end of the trip:
  • Bear vault
  • Hammock (I liked the idea, but it just wasn't practical most of the time)
  • Extra sneakers (But, I recommend light hiking boots for riding and closed-toe sandals for off the bike)
  • GPS for navigation (I used a GPS logger to record my route)
  • Solar charger (It never ends up working for anyone)
  • Tarp (I would have liked a small tarp at times (4'x6'))
  • Frisbee
  • 50mm fixed lens for my camera
  • Small binoculars
  • Clipless pedals - After having problems in Mexico I stopped using clipless pedals and didn't miss them!
  • Odometer - After losing my odometer in Mexico I decided I was better off without one!
  • Map distance measurer - probably better suited for hiking with topo maps
  • Second stove fuel bottle (just use a Coke bottle if you need to carry more)