Wario Deluxe is definitely my favorite of the finale stages, because not only was it surprisingly climatic for WarioWare (Which is a nice change of pace from the typical silliness that we're accustomed to from final Wario stages), but it's also neat to see Wario act like a villain again for the first time in awhile.
Also the track that accompanies the stage is fucking amazing shit.
Besides that though, I'll say the Wario-Man scenarios from Touched/Twisted due to just how memorable and silly they are.
For me it's definitely Wario Deluxe too, because it feels like a true final boss level with an awesome track to go with it that gets your blood pumping. And I just love how badass Wario is in this one.
My vote goes to Wario Deluxe as well, it takes longer to get going in terms of speed, compared to the other ones, but once it does it's every bit as frantic as the others.
Plus of course there's the major factor of it really feeling like a final battle, especially when Wario starts to take the prompts away from you for a few turns, that's something no other, regular stage in the series has ever done and it's just all around a very satisfying and even climactic final stage.