As far as I know there is no WW II rpg, except for Weird War II, but it's a supernatural style WW II and not historical WW II. But I'm sure you can take the supernatural elements out of it.
Yes, there is a linne of products for 3rd edition. Most of the books are available as PDFs.I think GURPS had a WWII branch.
It will DEFINITELY work. There was a supplement for Top Secret SI called COMMANDOS that outlined para-military, special forces and police backgrounds for agents, however the rules were so in-depth you could actually run a commando unit campaign (I did that when I was in the Army and 9 out of 10 Soldiers agreed, it was awesome.)<SNIP>
Top Secret might work. You'd be playing special forces types anyway and the agents fit that bill.<SNIP>
GI Joe with the serial numbers filed off Strike Force 7 [Spycraft] Strike Force 7 - Super Genius Games | RPGNow.com
A review of it Modus Operandi Spycraft Review: Strike Force 7
It uses the Spycraft engine for its rules.

(Dungeons & Dragons)
Rulebook featuring "high magic" options, including a host of new spells.