In addition to the above, don't forget to check out comic books. Sgt. Rock and Capt. America (and many of his associates) have all kinds of scenarios you could get miles out of, especially if you venture into the "weird."
For instance, both the Nazis and the Japanese (OK, and the USA and probably other major powers as well) had all kinds of secret weapon projects: we all know about the research into atomic bombs, jet planes and rockets, but there were all kinds of things like vortex cannons, superguns and other exotic programs. Adventuring to destroy an Axis research facility would be kind of cool...as would testing new advances from Allied "eggheads."
Then, of course, there is the legendary occultism of the upper-echelons of certain branches of the Nazis. Like the above, stopping Nazis from collecting the Spear of Destiny, or preventing the Japanese from summoning actual Oni to wreak havoc on the Allies would be fun.
In addition, the intersection of the two is kind of the ground where comics dwell. Super-soldiers, haunted tanks and the like are staples of Marvel & DC comics set in WW2.
Among the RPGs, check out Godlike for more scenarios, esp. if you venture into the weird. In addition, while Paranoia is over the top, its emphasis on secrecy and testing of newfangled gadgets are themes that could play well in this campaign. Of course, also check out resources like Ultramodern Firearms D20, Spycraft, and the like.