I'd have to say 2005 because it was rated at 245 HP and 287 lbs of tq compared to 06+ of 236hp and 270+lbs of tq lolz.
Seriously though, it depends on what u want outta the truck and that's all. Like already mentioned the 2005-08's have an eaton clutch style LSD, are compatible with the X-1 engine controller along with the E85 668cc primary injectors and 7th injector(u can run E85 thru the TRD blower and get anywhere from 30-40 extra rwhp from E85). Downside is no side curtain airbags, no stability or traction control and no head rests for the rear seats.
The newer models have their pluses which are more airbags(safer), backup camera, stability control and traction control, and the rear seats are more comfirtable from what I hear and they also have head rests so the passengers head doesn't smack the glass. Downside is the ECU harness change so no X-1, and the weak ass open differential.
So ya see it really matters what ur interested in, power with either a TRD blower with every option there is for it, URD MKIII blower making over 400rwhp and a real LSD or safety and only having a stock TRD blower for added power(yes u can still add an intake and full exhaust to the 09+)