Just for my own personal reference, and because it's fun to think about: The canonical 3D sonic games, in order, seems to be Sonic Adventure, Sonic Adventure 2, Shadow the Hedgehog, Sonic 06, Sonic Colors, Sonic Generations, Sonic Lost World, and Sonic Forces.
It's interesting because when you take the games as a single cohesive timeline it's clear that there aren't actually that many "bad" sonic games.