Siskoid made the claim that World War II is the best known war. I'd like to note that that attribute has some roots in something Chris said in that WWII "was the last 'good' war" fought and won by the US (and its Allies). Other conflicts, as mentioned, weren't so seemingly tidy or clear cut. It's a no-brainer that comics would be much different had WWII been lost.
However, an interesting corollary to this was mentioned by Chris and Smacky with Transformers and Iron Man taking place during the current Iraq and Afghanistan Wars, respectively. Granted Transformers wasn't centered on the war, just taking place in the area for part of the movie. Tony Stark allegedly has a run in with Osama bin Laden in Iron Man, which could possibly be chalked up as a bit of propaganda but I haven't seen the film yet.
With WWII being the first and only mass media war to be won by the US, it was essentially romanticized, as Siskoid mentioned, paving the way for creative liberties like monsters and such without much of a fuss. This is one of the reasons we haven't seen much in the way of Revolutionary War or WWI weirdness.
For now, WWII remains the virtual golden child where bizarre war fiction is concerned. While we might occasionally see anomalies, it's pretty safe to say the widespread wackiness inserted into WWII won't ever be repeated with conflicts since.