I personally, have to agree with one of the first previous posts and say for some reason, I have always been partial to the N64 controller. I don't really know why, it just seemed to adapt to my hands well. My only issue with them is that their analogs die out easily, thus killing their sensitivity after a year or so. I enjoy mine so much I purchased a USB for some PC games and emulators. Just my preference haha, although I wish I could find one that supported force fedback.
As for the PS/PS2/PS3 controllers, I agree with most of the others. They take some getting used to, and then you'll eventually be comfortable with them. I guess for those who have been using them since PSX, its a no brainer, but I can understand where your coming from with the akwardness.
"They're everywhere, the little harlots."
-Martyn