For 3D - Sonic Unleashed. While Sonic was known for speed more than platforming on the Genesis, the Hedgehog engine in this game got the sense of speed right.
In 2D - Knuckles Chaotix - Sonic Colors/Rush Adventure/S3&K were going to end up in this spot, but the 32X game is my long time favorite. For two reasons: Unique gameplay with two characters, and the fact that it's damn near impossible to find now. SEGA, if you're still looking for games to celebrate Sonic's 20th in any form, rerelease this game on XBLA/PSN. It's a classic however you slice it.