Was just thinking about this- I really, really love the final dungeon of Super Mario 3. It's not the hardest or the most graphically impressive. But for whatever weird reason, I really love that dungeon. I like all the alternate routes and this one part after you reach the top of some stairs- there's a little spot to rest and nab a hidden 1-up. It's like the halfway point. And the fight with Bowser was really fun and memorable too. I love pretty much all the final dungeons, but Mario 3 is my fav.
I know it's not technically a dungeon but I really love the Rainbow Roads in each Mario Kart game. They're stunning, breathtaking, gravity defying and a cruel fickle mistress.
I like the one in super mario 3d world. With the neon theme and climbing to the pow block. I like it mostly because it different. Plus the world music is great.
Mario World. I just love the different paths you could take to get to Bowser. It gave some great replayability to that dungeon.
Does Paper Mario count? Final Chapter of TTYD plz. If not, for 3D game? Uh... Probably Mario Galaxy's final boss level. 2D? For some reason I want to say Mario Bros. U. I don't know.
Those final bonus levels they've been adding to 3D Marios are really good, even if they're insanely difficult.
Alright, I've been playing a lot of retro Mario lately so I'm in: And you know what? I gotta agree with Mako. Mario 3 really hit it out of the park, I also like the "false Bowser" part where you can beat Bowser, then fly over the right wall and fight the "real" Bowser. Crazy.
The final world of Super Mario World and the final level of Super Mario 3D World basically show off the showy, over-the-top egotist side of Bowser that I really love... sooo...