Sonic 2 is my favourite 2D Sonic. For 3D, Sonic Generations and Colours.
I would have enjoyed Colours more though if it didn't have some of the weird power up abilities. Some where okay, but there was others that really disrupted the gameplay flow for me and were awkward to use. Still a great game though and one of the most polished 3D Sonic games!
Generations was really cool, just takes my top spot. I love the mix of old and new and it felt like a mix of all the good things that makes Sonic great in both dimensions.