I'm a fairly big game geek and I can't think of any game involving the scientific method. A few of the games that might come close or would at least be interesting to some people on this thread:

Mindtrap - plays a bit like Trivial Pursuit, but with braintwisters, lateral thinking and logic puzzles on the cards. Things like "how many months have 28 days" (all of them) or "The maker doesn't want it, the buyer doesn't use it, and the user doesn't see it. What is it?" (a coffin).

Clue: The Great Museum Caper - almost completely unrelated to Clue. One player is a thief that moves secretly around the game board and the other players try to catch him. (Unfortunately I see it's out of print and priced sky-high on Amazon.)

Settlers of Catan - several educational positives: probability lessons, trading with other players, more than one way to win.

Outdoor Survival - an old Avalon Hill game. Not that great of a game, but interesting just because of the topic.

Blink / Set - two pattern-matching card games.