Assuming you have the V6:
1. Headers - Doug Thorley Long Tubes. I have them on mine. Bolt-on simplicity. Works great even though they're listed only for Taco's and FJ's. Check my sig.
2. Intake - TRD/aFe (more or less the same), Volant, True Flow, K&N (I'd pick this last).
3. Exhaust - TRD, Magnaflow, Gibson. *** Y-Pipes are also a good upgrade. Check yours out as it crosses around your tranny. Pretty restrictive, huh?
4. Programming - Allan Phillips Racing - APR X-1 Computer. Fully programmable with new exhaust cam gears (improves volumetric efficiency). +30HP & +20lb.-ft. improvement alone out of the box.
5. TRD Supercharger - With the APR controller, the TRD supercharger can be simply bolted on and programmed to a full custom tune. The fit kit (intercooler accessories) from either the FJ or Taco with take some extra creativity fitting in place.
6. Fitch Fuel Catalyst - Improves and conditions your fuel prior to combustion. Supposed to guarantee around a 2mpg improvement as well as a power increase. Verified to work by third parties and so far the Australian gov't will subsidize purchase and install one these in Australian cars.
These are just a few to start. A lot of stuff can also be picked up from
URD USA