For me, it depends on what controller it is. I'm trying not to sound like an XBox Fanboy here, but I do think the 360 controllers are a hell of a lot more comfortable than the PS3 Controller or the Wiimote.
I do enjoy playing some PC games aswell, though, but if I like using the mouse depends entirely on what game I'm playing. For example, when playing, say Fallout 1, FAllout 2 or Fallout Tactics, I think the mouse is a good way to control everything; but I dislike playing games like Halo or Mass Effect on the PC because I feel games like those can't function properly without a dedicated conrtol system.