Tom Hinshelwood offers a set of free wargames rules called 1945, for games set during WWII.
Other Resources:
Rules: WWII
Bombs Away Carrier Game
Bombs Away is a simple, three page print-and-play game about carriers in the Pacific.
Blood Red Skies WWII Aircraft Rules
Warlord Games has a free version of its Blood Red Skies WWII Aircraft Rules.
Mustangs Air Combat Rules
Mustangs is a classic Air Combat game from Avalon Hill which, like most of their great systems is long out-of-print. Warflag, however, has a set of rules for playing the game in miniature.
Naval Action
Naval Action, by Lou Coatney, is a set of free wargames rules for miniatures battles in the World War II Pacific Theatre. The page also provides some markers to use in place of model ships.