I recently wrote this up for a buddy who is shopping for one, based off my own experience with owning one. Anyhow, figured I'd post it up here in case anyone else cares (or if anyone else wants to add to it or correct anything I wrote).
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00-04 are cheaper, but have substantially less power, smaller brakes/wheels, and one less gear in the transmission (and some goofy cosmetic things). You can find these dirt-cheap, but unless you're on a very low budget, I'd pay extra for an 05+
05-07 have more power, better transmission, bigger brakes, and look better (in my opinion at least). You should be able to find a pretty nice one with under 150k miles for well under $10k, if not less.
Mileage is generally not a concern if well-maintained.
Frame: check for rust (preferably with a small hammer, since it rusts from inside and you can't always see it). From what I can tell it's usually driver's side in two main places – right around the middle of the truck near the transmission crossmember, and also look at the frame inside the driver's front wheelwell, toward the back section of it. Other areas could be an issue too, but this is where I've usually seen it. In general, just try to buy one from a non-road-salt area if you can. There should be a heavy front skidplate, and it will almost certainly be rusty, but still pretty strong.
Body: not generally rust-prone, but the front of the rear wheel arches is a trouble spot. It's hidden by the back door, which has a lip that goes over it – so open the back doors and look down at the bottom front of the wheel wells. That's the only real body rust area I know of. The tailgate handle is a problem on these since the interior mechanism is weak and can bend. You can get new ones on ebay for cheap, or take it apart and modify it yourself. If it is bent, the tailgate may be tough to open. But, you can roll down the rear window with the remote or the key (only rolls UP with the key, oddly).
Engine: timing belt/water pump. If they don't have records, do it ASAP. Air injection pump can go bad, but if it has over 100k miles there's a good chance that's already happened and been fixed. If it does go bad, you can get a bypass for like $150. No other big problem areas on this engine that I know of offhand. If you hear a “ticking” sound under throttle, those are usually pinholes in the header flanges. Doesn't hurt anything, but a bit annoying. Otherwise, these trucks are well-insulated and generally very quiet when driving. You can buy aftermarket headers that make pretty good extra power, if you're so inclined.
Transmission: If you're towing, do a fluid change. But generally they're pretty stout, especially on the 05+. Never tow in overdrive.
Diffs, drivetrain, etc: Just typical Toyota stuff. Change fluids and grease U-joins and slip joints and you're good to go. Oh, 05+ has a center locking diff. Don't think the 02-04 does. It's activated by a button on the dash when in 4WD. Test the 4WD on a straight road. If it hasn't been used often the grease can get dry and it may take a few seconds to actually engage and then will with a “thud.” This isn't an issue and will resolve itself if you put it in 4WD periodically.
Electrical: no common issues that I know of
A/C: Most of these have a rear A/C condenser as well. It will have controls both on the dash and for the back-seat passengers. Generally if the main A/C works, the rear will too. If A/C is not cold, could be a leak in the line going to the rear (mine had this issue). This is a hassle to replace, but not very expensive. These trucks have COLD A/C when everything is working properly.
Brakes: The front calipers are 4-piston and if they're original, they could have one or more pistons seizing – you should be able to feel it in most cases. You can buy brand-new calipers on RockAuto for cheap (or reman'd), or they're easy to rebuild. The brakes are “ok” for a truck this size, but make sure you get some good HD pads that can deal with heat if towing. I actually use Hawk HPS (Tundra fitment). I haven't done it, but the even larger 4Runner SportEdition front brakes can apparently be fitted with little to no modification, according to the internetz.
Wheels: 05+ should have 17” stock wheels. Stock tire size is 265/65/17, which is probably best for towing. 265/70/17 looks better but hurts towing a bit. Definitely used LT-rated tires. Load Range C should be sufficient for most tasks. I have load range E which are really, really heavy. The original tires I think were actually P-rated, which is fine for general driving but too soft if you're gonna tow, haul heavy stuff, or spend time off-road.
Interior: the design is pretty dated-looking but overall everything is good Toyota quality and I haven't had anything break at all. Btw, jack and lug wrench are hidden in a compartment under the passenger-side middle-row seat. You need a thing in there to lower the spare via a small hole in the back when the rear hatch is open. Spare is underneath. Driver's set tends to get some rips and cracks in the leather on the bottom section.
Suspension: all pretty much standard Toyota stuff, much of it crosses over with 4Runner, Tundra, etc. Bilstein HD shocks fit well and are a big improvement. Air-Lift air bags for the rear are cheap and make a big difference when towing, if you don't buy a Limited (which has factory air bags). Also, get some urethane steering rack bushings, they tighten things up. Front suspension bushings seem to hold up well past 150k miles at least.
The lower front balljoints on these were a recall item back in the day. I would expect they've been replaced by now on most, but if not, DO THAT. They bolt on to the control arm, so it's not too hard. Make sure you buy OEM TOYOTA ones, not aftermarket. This specific part this is pretty important. Otherwise, you can do bushings or whatever, nothing too fancy about any of it. Steering rack urethane bushings are a nice upgrade for cheap.
Headlights when old can get foggy/yellow. I generally just polish mine every couple months. You can buy new housings pretty cheap. Headlights on these are “ok” but not great.
If the tailgate window doesn't roll down, it's almost always a dirty sensor in the weatherstripping, so just clean it.
There is an airbag recall on these things, like most vehicles these days. Both for passenger front airbag as well as side-curtain airbags (different recalls). So you can check if they've been done via a dealer.
That's about what I can think of.
Photo for the hell of it