Favourite would be Sonic CD (J) tied with Sonic 3 & Knuckles. They both have vivid environments and amazing music. Sonic CD took the series in a different direction, with bosses that are more difficult to hit (but with a lower hit count) and time travel. Sonic 3 and Knuckles had about the same amount of ground one could cover, but laid it out in a linear fashion. It used a huge variety of themes, and three characters to play with. And both Sonic CD and S3&K used pseudo-3D special stages, where the objective was not to collect Rings, but to find and transform a number of objects. Blue spheres turned into red spheres (or Rings), and the flying UFOs turned into flaming wrecks.
... And the worst has to be Sonic Jam for the game.com. I think the reason it hasn't been mentioned yet is because people have repressed memories. It was buggy, had a terrible framerate, was hard to see due to the screen, and was an extremely poor rendition of the Genesis games it was based on.