In the main campaign, and excluding boss levels, my least favorite used to be Red Volcano Zone. But as I've gotten better at the game, that level has become more and more fun. In fact, most of the levels have become more fun as I've gotten better at the game. Castle Eggman Act 2 in particular has really gone up in my rankings... once you really understand the mechanics and physics of the game, CEZ Act 2 transforms from a cruel gauntlet into an exciting playground.
As of right now, my least favorite standard act is probably one of the Egg Rock acts. There are some sections that still feel just a little too hard, with no alternative route available at the time you get there. Specifically, I'm thinking of the rapid crusher hallway (that Tails and Knuckles can skip) in Act 1 and the disappearing platforms section near the end of Act 2. I think Egg Rock could use a few more branching paths accessible to Sonic.
As for boss levels, my favorite is probably Black Core Act 1 (I failed it several dozen times in my first playthrough, but it's pretty fun to replay), and my least favorite is probably the Arid Canyon boss fight (it feels a bit too unpredictable and a bit too wait-centric).
Including all levels in the unmodded game, my least favorite has got to be either Aerial Garden or Azure Temple, though I only played the latter once, so I'm not sure how I'd rank the two in comparison to each other.