Haha, yeah, it is hard to make a list like this.
My three favourite Pixar films have been "Ratatouille" (easily my favourite), "Up" and "Monsters Inc".
My three least favourite were "Finding Nemo", "The Incredibles" and "Cars". Something about those three just didn't click with me in the same way that the other ones did.
I love the Toy Story films too, of course, but I genuinely believe that Ratatouille is Pixar's masterpiece :P