The first two of the new Narnia movies have a bit more war stuff than is present in the novels. Prince Caspian might still be a bit dark for young kids, though.
It might be worth checking out any movies based on Noel Streatfeild books? Ballet Shoes and so on? Most of her books, IIRC, are set casually during the war - the kids carry gas masks and talk about rationing and stuff. One of her books, When the Siren Wailed, is about evacuees, three siblings from London who go to the country... I believe my childhood copy had a "Now a BBC... something" cover on it. Don't know if it was a movie or TV show, though. Anyway, it might all be a bit girly for your sons, but it could be worth a shot?
Honestly, though, most WWII films will and should be too intense for a three-year-old! It's meant to be dark; it was one of the most horrific times of recent history; and it shouldn't be cutesied up, you know? I can think of several WWII films with light moments in them - La Vita e Bella, Mrs Miniver, The Great Escape, Mrs Henderson Presents - but they all show the horror of war in one way or another. I think to some degree, it's subject matter that's just inherently unsuitable for little kids.
That said, DH says that some of the Biggles books are set in World War II, although most are WWI. Your kids might go for that? There's also Chicken Run, although I guess the analogies would go right over their heads! And there's Sky Captain and the World of Tomorrow, which is kindasorta set in WWII... it's dieselpunk...