Any list of this kind is highly subjective, especially given the huge number of WWII films out there. Breaking the question down into subject categories simplifies the problem a bit, though it still means making difficult choices. Some examples of category nominations (using films not already mentioned)
Best submarine movie:
- The Enemy Below (1957)
- Run Silent, Run Deep (1958)
Best convoy / escort movie:
- The Cruel Sea (1953)
- Action in the North Atlantic (1943)
Best film about the responsibilities of command (in both cases, of a bomber group):
- Twelve O’Clock High (1949)
- Command Decision (1948)
Best film about planning and executing an “impossible mission”:
- The Dam Busters (1954)
- The Guns of Navarone (1961)
Best film about the Resistance:
Most frightening Invasion-of-England film: