I'm surprised this thread isn't popular. I can't possibly pin down a favourite in the venerable Wario Land series. BlueJack had the right idea of listing each title. They're all unique, with not a bad game in the bunch.
Anyway, you've probably noticed I always defend Wario Land: The Shake Dimension. One of the key reasons is, I think it has really,
really underrated level design.
Every Wario Land brought something new to the table, and Shake Dimension was
no exception. Any man and his dog can clear the levels casually, however, if you burrow into the meat of the game and try to accomplish the countless "missions", you realise just how much depth and complexity they built into everything.
It
forces you to look at levels in multiple perspectives and think about how many missions/treasures you can knock off in one visit. This gives you an actual reason to return to levels and have more fun with them. The designers didn't slack off.
Combine that with all the escape time records, no damage missions, and everything else... whoa, mama! This game has more replay value than just about any platformer I've ever played. It truly deserved some actual love and attention back in 2008. If you like Wii games, give it a chance!! It's a true work of beauty.