Season Two without a doubt - it was the most dramatic without being crazy (Meredith coming back from being pretty much dead with no side effects anyone???), it had great character development, some really cool medical cases (I felt season 3 kinda forget that they were in a hospital) and it was funny! I just loved season 2 so much, I'm hoping season 4 is gonna be as good! I did like season 3 as well though, just not as much... and season one was too short!
I still have to watch season 2. I didn't start watching until the beginning of last season. I just finished watching season 1 & will be watching season 2 very soon. Once I finish I'll let you know what season I think is the best & why.