Humor in games seems only a problem with Western franchises, where being gritty and gory is almost a requirement. Anyone who's played a few Japanese games -- Katamari Damacy, any of the Mario RPG series, for instance -- will see that they've become quite facile with humor in a game context.
In Gokujou Parodius there is a point in the high-speed highway level where a "falling rocks" type road sign will appear, and moments later rocks will tumble out of the sky to crush your ship. Then a "deer crossing" type of sign will appear and you have to dodge the hail of falling deer. After that a sign with just an exclamation point appears, and I bet you can guess what happens next.
Three massive exclamation points tumble out of the sky.
It was one of the funniest things I'd ever seen in a video game, and I laughed so hard I was completely thrown off.