The term UFO was not around during WWII. Allied pilots had to give them some sort of identification and Foo Fighter was what they used. Today they would be UFO's.
Found this, the Nazi's were apparently experimenting with advanced gyroscope mercury technology at the time, (nevermind the UFO connection in the video) http://youtu.be/ycOw4Gsf6bc
My Grandfather had a good friend who was a tail gunner on a B-17 in Europe. Growing up in SW Missouri he'd seen the "will-o-the-wisp" before. He also saw the Foo's. He said they looked exactly the same. Except the Foo's moved around more. So if you want to believe an old man who's been dead for 25 years, it was an electrostatic phenomena.
Many years ago in elementary school, we took a trip to a senior citizen home and had to interview one of them. My guy was an old vet, and we talked about his life and the war. I was born to crazy, so I knew about crazy and none of his story seemed crazy or hinted at him being loony.. he was normal for the most part. Then at the end he whispers 'no one will believe it, but there is a base under Antarctica' and when I asked if it was ours, he just smirked and shook his head. That was all I could get out of him about it, so it could of just been he heard a rumor within the military and that was all he knew of it..
As in no.. it wasn't our base. We had to spend all day there, talking.. and growing up I was obsessed with space and Star Wars/Trek and aliens. So the fact that he wouldn't tell me who's it was made me think he was talking about aliens with that smirk he had.. or he could of just not known cause it was only a myth. Don't know, but if one of the world powers hasn't built something hidden there, even if it's not some sinister thing, I'd be surprised.