THIS POST WILL CONTAIN SPOLIERS! You have been warned.This is such a hard question.
I like the second season I would say.
The first season was a little bit too 'we're starting up and explaining everything to you'
The third season I didn't like the whole thing with Tritter.
Fourth season was a massive overhaul and it did seem like they were trying to sort a 'we're completely revamping this' until later on when the old guys were still there. Although the two part season finale was amazing.
Five was quite 'back to business', which they already did with two (obviously up until Simple Explanation, but then it was overly heavy on the drama; although the Amber scenes were priceless).
Six I didn't really enjoy as much, felt it was too mixed up and the season finale was a hugely dramatic way of getting to where we'd all waited 6 seasons to get!
Seven was all rosy followed by a massive blowup in Bombshells and then just back to normal again until the finale, which made no sense (but did set it up well for Lisa Edelstein to leave)
So I am saying Two because I feel its the first time it was properly 'House' in the way I really liked it. The characters were well established, we were somewhat immersed into the medical terminology and the whole thing seemed to flow well. Season 5 comes in second because it has this whole same feel until the end, and season 1 in third because you started to get that towards the end once they'd properly introduced us to the concept.
Woah, long post