Best: Paper Mario: The Thousand-Year Door's Rogueport for its style. Toad Town makes you think that aside from Bowser, there's just no bad anywhere out there in Mario's world. Then you see this town, which at first just seems absolutely horrible. Gang activity, pollution, graffiti (and not magical graffiti either), it's all there. Also, the Piantas were cool in this game and this game alone, being the mafia and all.
Worst: I'm afraid I may have to say Super Mario 64's Peach's Castle for its lack of life. There were no Piantas, sure, but also no Piantas I could annoy.
As for Flipside and Flopside, they're really annoying to navigate, but what can you expect? It's in 2-D.