IMO wario's best counterpick would probably be rainbow cruise. It brings out the best of his aerial mobility, his insane DI and, of course, his aerial combat. But of course you don't wanna be picking that against Dedede because he gets a semi infinite on the boat and some walk-offs for easy chaingrabbing to death.
So often you should have a second counterpick against characters that may beat you on your normal counterpick stage. For example, I main falco and my normal counterpick stage is Jungle Japes. However I'd probably get beaten there by ROB because I can't chaingrab him or spike him into the water because he can easily survive, so against ROB I would probably either go battlefield or Final Destination.
So yes like Niv said it's important to figure out the strengths and weaknesses of your character and the opponent's character, and pick a stage that caters.
Edit: Wario's best neutral stage would probably be battlefield because he dominates the platforms with his aerial movement, quick attacks and his rising bite. So try and get it as your neutral stage and keep it as a secondary counterpick.
Edit 2: I was looking at the wario weekly stage discussion thread, which can be found here:
http://www.smashboards.com/showthread.php?t=182253
I saw that Japes was also a very good stage for wario, particularly with his bite into the water. Have a read of the thread, but remember not to pick Japes against me when I play falco