Best: Xbox 360, Gamecube
Worst: Dreamcast, Original Xbox and Sixaxis.
Personally, I never found DS1 or 2 particularly uncomfortable, definitely didn't fit my hands perfectly, but Sixaxis (and I guess DS3) is a joke.
Why? L2 and R2 buttons. Had they extended the bottom of the controller to accomodate this new addition, we would have had a bigger controller that would have fit more comfortably in more peoples hands, instead we get a smaller controller (bottom surface area wise) so that less people will find it comfortable.
Note: There is a difference between acceptable and comfortable. For alot of people, it's the former that's true but they confuse it with the latter.