I fell more comfortable with PS3 analogue control, but to be honest, the most comfortable control I've ever used is the N64 one.
I was always and am still a fan of the GCN controller myself, but I remember someone once refer to using it as "trying to game on a piece of tree bark". Never understood that.
And I'd have to agree with Maedhros, I find the 360 controller is better than the PS3 controller for everything but platformers...and racing games.