I have the aFe Stage II Cold Air Intake, which after a month of reading I found the best reviews of. It is basically the same as the old style TRD CAI; I also have the aFe helical throttle body spacer, but I've been told it doesn't do much. I can't say for sure because I put it on at the same time as the CAI, I think I paid $315 for the CAI and $80 for TB spacer.
I also have an Underdog Racing Mass Airflow Recalibrator which also has great reviews and is tuned by Gadget at URD according to what other mods you have, but I am debating on upgrading to the APR X-one programmer, unfortunately it is about $1,500 (the MAF Cali was about $300). As far as I know, and I have searched a lot, that is the only programmer available for the V6. You could get a Jet Chips V-Force, but from what I read it doesn't really do anything for performance and is more of a monitor.
A tuned exhaust like Magnaflow (~$400-600), or Borla (~$800-1K) if you have the money, will also help. I had a Borla turbo muffler (p/n 40653, $110) on mine and gained about 0.5 mpg so that prolly indicates some HP gain. I took it off though cuz I got tired of it being loud under 2K RPM, the way it is tuned it sounds fine after 2K. The V6 just doesn't sound good like a V8 does IMO.
If you really want it you can also get a supercharger for about $5-6K, I can't think of who makes one off of the top of my head but there are a few. But as far as I've found that's about all you can do for the V6.