For me the best transition was Final Fantasy VII. It was the biggest reason I switched from Nintendo to Playstation. I'd always loved Final Fantasy, but VII really took it to a whole new level.
For me the worst transition was Mario 64. That was the other reason I switched from Nintendo to Playstation. I just really, really hated that game and the N64 controller, and I still do. I think of Mario 64 in the same way that most hardcore gamers think of Wii Sports.