Story line is mainly apparent in games that go through the trouble of getting it, most new shooters don't care much, because, well, it doesn't matter much for a shooter. Half-Life kind of started an unfinished trend, they had a god story, involving, yet almost no other game had a good storyline after that.

If you want GREAT story, you should play Planescape: Torment(My absolute favorite in story, characters and even humor, it's got loads and loads of very good humor, mainly in conversations with your party NPCs).
Another one to consider is Fallout, which has a great atmosphere, and some good grim humor here and there put into it.

Making a game which runs along the lines of humor will almost always be an adventure, because it's hard to imagine a game where you shoot loads and loads of enemies row after row as something you put humor into, nor is it likely that you put humor into the war/strategy-game with a serious backtone, it wouldn't fit.

That's also something I like about games, and something that makes games good: atmosphere. THat is also something I miss, a strong atmosphere, most of the modern-day games don't HAVE any atmosphere, it's all just mainstream general stuff you've seen millions of times. *sigh*