Something that gives many authors difficulty when writing is laughter.
In this case, I don't mean making the audience laugh, although that's tricky enough. What I'm really talking about is characters laughing.
Now, there's a lot of reasons a fictional character might laugh. Relatively rarely do they have to do with something being funny. More frequently, particularly in cartoons and comic books and the like, we see characters laughing because they're confident in some kind of plot or have just enacted terrible vengeance. This, obviously, is villainous laughter.
The primary difficulty with villainous laughter is that it can be difficult to convey laughter in a convincing way on a comic book page. Also, some people find it to be a trope of certain genres or to be cartoonish or silly. (And what, may I ask, is wrong with cartoonishness and silliness?)
On those relatively rare occasions where characters are laughing at something they find funny, writers often fall into a trap not unlike the trap of small talk: Uninterestingness.
In the audio commentary for Pixar's Monsters, Inc., one of the commentators remarks that if characters laugh, it has to be funny for the audience, too. This is generally true. If you can't laugh at a joke, then there's no reason your characters should (keeping in mind how well the joke works in the medium you're working in).
There are actually a few exceptions to this rule, and they rely on how you play the joke (or other form of humor-I'll stick to "jokes" for simplicity's sake).
The first exception is to, through narration or another means, admit that the joke isn't very good, and have at least some characters criticize it or otherwise fail to be amused. For instance, I very clearly recall that in some story or another (I don't remember which, sadly), a character is giving a lecture, and a person in the audience makes a "smart remark." The narration then refers to the "smart guy" by the term "wag," indicating that the author didn't take the joke to be funny, despite the response from others in the audience. (This sounds like something that Isaac Asimov would do, but I can't be sure.) Note that some readers will be critical of such a move, so you should be judicious with this method.
The second exception is character-based, and sort of similar to the above method: Have a character who is a bit of a flake laugh at it. We can see this (sort of) in the "Fish-Eaters Anonymous" (Fish are Friends, not Food) meeting in Finding Nemo. The mako shark, hearing what he thinks is the punchline to Marlin's attempted joke, cracks up, admitting a second later that he doesn't get it. (If it had been a real joke instead of an interrupted one, it could have been played exactly the same way.) Flakes can also be lame pranksters or something similar in this respect.
The third exception is in the timing. I'll refer again to Finding Nemo. At the end of the movie, we finally hear the punchline to the joke that Marlin has been trying to tell the entire movie-and we never hear the entire thing. Yes-acceptable laughter by omission.
Of course, generally speaking, depicting humorous laughter within fiction is just as tricky a situation as humor itself. Your mileage may vary.