Jak and Daxter by far, in every way. The variety of gameplay, the awesome story and scripting, the atmosphere, the feeling of being in a world.
I also prefer Crash to Spyro and Uncharted to Resistance.
All in all, Insomniac and Naughty Dog are the only reasons I picked up a PS3 over a 360. As they, IMO, are the best developers (perhaps of all time). Third = Valve.