Excluding the obvious ones (New Pork, 75m, Mario Bros., Mushroomy Kingdom I & II, Rumble Falls, and the Melee stages) that's a tie between some of them.
I forget that Mario Circuit exists, so I don't end up playing it, but it's a poor stage, so I wouldn't anyway. I used to play on Halberd, but it's pretty ugly and not too fun anyway. Pokemon Stadium 2 I never play on, simply because it's inferior to the first one, because of the wind tunnels it has. Spear Pillar is just annoying, and you're stuck inside the tunnel most of the time so KO's don't work properly. And Skyworld, I used to play on, but I feel it's too annoying now.
My favorite stages in terms of gameplay (shame the first two are banned) would be Summit, Warioware, and Delfino. Summit is the most beautiful stage bar none, and simply for that. Warioware is actually incredible fun for casual matches if you get over how unfair it is and actually play the microgames. Delfino is incredibly relaxing with the combination of stage design and the music (mostly the music).
