I think the smaller Xbox/360 controllers tie with the Wiimote for most comfortable and useful. I think it's the perfect design as far as traditional controllers go; the sticks are easy to handle, button size and placement are sensible, the triggers break cleanly, and it's ergonomically well-designed. (The original Xbox controller was, of course, an abomination.)
I'm ambivalent about the N64 controller. The stick and Z-trigger are cool, but the trident design is terribly foolish. And the GC controller was even worse, with its ridiculous XYZ placement and oversized/undersized A/B buttons. The sticks never seemed to work as well as those on PS2 or Xbox, either. I hated playing traditional FPSs with it, though Metroid worked beautifully.
The DualShock is just okay. Nothing terrible, but nothing outstanding - the sticks are a bit too far down, the triggers are too shallow to really break cleanly, and the handle design can get a bit uncomfortable after a long sessions. It's like the Xbox design team looked at every flaw and improved upon it. I haven't used a Sixaxis for a couple of weeks, but I remember it felt better than the DualShock.
And yeah, I don't get the Wiimote complaints. I'm holding one right now, and I honestly can't find any sharp surface to dig into my skin. It could do with another face button, but on the whole it's clean and comfortable.
