I'll freely admit it--I'm a crossover junkie, in part by taste and in part by necessity. As such, I read a lot of them, and I've seen some real gems; some of my favorite fanfics (e.g. the X-Jedi series) are crossovers, and well-written crossovers in general serve as missionaries for the worlds they bridge (X-Jedi, for example, was my initiation into the X-Files).
(Parody crossovers, of course, are another matter, one outside the scope of this rant.)
Sadly, the vast majority of crossovers are pure, unmitigated crap, and in the remainder, even where the crap is mitigated what's there is often enough to ruin the reading experience. I know people who, overwhelmed and disgusted with the deluge, have sworn off crossovers altogether, which I consider a tragedy.
And I know exactly where to lay the blame--on the legions of amateurs who, in search of some undefinable level of "coolness" somewhere in their own small minds, have managed to sully an entire genre with their incompetence. And for them, I have a number of complaints (which I'll disguise as tips in the hope of perhaps saving a story [or the prospective vict--er, readers of one]):
Basically, have a reason (by which I mean developing characters or concepts, that you think it's cool) for picking the universes you cross over. If you don't have a reason, DON'T DO IT.
On a tangent to this, I'd like to make a suggestion:
I'm sorry, folks, but just about every conceivable, or even remotely plausible, X-Files crossover has already been done, from Star Wars to Star Trek to Highlander to (I kid you not) Final Fantasy VII. Crossovers (for reasons I'll get into shortly) have fewer possible plots open to them than most other fanfics, and with the X-Files, almost all of them have already been used. Unless you're a veteran author whose works routinely become classics in their respective fandoms, I'd suggest you heed this big red flag I'm waving around and leave Mulder, Scully, Skinner et al in peace.
Now that you have two universes selected to cross over (yes, it's possible to do a crossover with more than two, but for novices that's the equivalent of a six-year-old trying to lift a five-hundred-pound barbell), you're ready to start plotting. So the first question you have to ask yourself is:
It's at this point where you may be forced to scrap your story (and if it comes to that, I'm on my knees pleading with you to follow that conclusion and see where it takes you). You need to figure out some way for worlds to collide and champions to cross swords while at the same time remaining faithful to the basic rules, physics, and characteristics of each world. If you have to radically alter a basic characteristic of the world in order to accomplish the crossover (for example, restoring magic to the world of Final Fantasy VI after Kefka's defeat without any explanation) then stop, get up from your desk, and rapidly slam your head against the nearest convenient wall/door/katana/keyboard/fist/etc. until you've changed your mind (for that matter, this is a good rule for ALL fanfics to follow--there's nothing that will piss readers off faster than authorial fiat.)
If you've found a plausible way to accomplish the crossover, you can now start to formulate the plot proper.
For example, let's turn to that great-grand-daddy of overdone crossovers, Star Wars/Star Trek. Let's say you decide that you're going to cross over these universes by creating an intergalactic wormhole (a plot device which, those who have sampled SW/ST crossovers know, is by now a cliche among cliches). That wormhole should then become the focus of the entire story--all the action should happen because of it and lead back to it; if the Empire is invading Federation space through it (to speak of another cliche among cliches) and Darth Vader is trying to rape Counsellor Troi's mind through it (to further compound cliches) then at some point the Federation should discover its existence and, from that point on, seek to find a way to close it.
The same applies to any other crossover plot devices. If some mysterious force has brought characters from one world to another (not something I'd recommend under any circumstances, but still), then the author is honor-bound to 1)make that mysterious force the focus of events, if not the puppet-master behind them and 2)reveal the mysterious force's identity at the climax--in short, make sure that all the events in the story happen because of this mysterious force and lead up to it, even if the reason you wrote the crossover in the first place was to explore, in a hypothetical Star Wars/Final Fantasy VII crossover, the potential impact of the Force on Cloud's psyche.
If you don't do this, then the crossover becomes gratuitous and unnecessary, in which case you should go back and reread the first "tip," and VERY SERIOUSLY consider whether you're writing this crossover only because it "sounds kewl." If you are, then you're much, much better off replacing the crossed-over characters with new ones of your own design; it'll be good practice for you as a writer, and you'll save a fandom the trouble of slogging through a piece of what is, to them, extraneous drivel.
I'm deadly serious about this one--the purpose of fanfic is, to quote PS Pages webmaster James Maxlow, to "fill the holes, answer the questions, explain the unknowns...presumably, each of us has our own answers to those questions," and when you make a permanent change to the landscape of the world like this, you're answering the question for others. Crossovers are a means to an end; it's important to remember that. Making an alteration of this magnitude to a universe at the end of a crossover is as big a no-no as presuming one at the beginning of a crossover.
In short--don't end your story by wrecking the canon.
When I first wrote this rant, I had just recently run across a crossover between the X-Files and an old Saturday morning cartoon series...Captain N, if memory serves. I was absolutely ecstatic while reading the first part of the story; it read, sounded, and felt like a bona fide X-File, while at the same time treating the other world with all the respect and fascination worthy of a crossover. But about halfway through, the characters moved to the other world...and the feel abruptly changed from that of an X-Files episode to that of a cartoon. What's worse, the characters changed as well, and the story degenerated into a campy mess with which I became thoroughly disgusted. While I have to credit the author for her versatility, she hooked me with the prospect of an X-File, and she should have delivered the whole package.
All writers need to write to their audience. In the case of crossovers, this becomes something of a challenge, because you're writing to two audiences; you have to remember that half the cast will consist of nearly brand-new characters to half your audience--and the other half of the cast is composed of strangers to the other half of the audience. Write with too much familiarity on either side of the equation, and half your audience will end up completely and hopelessly lost.
The exception to this is when you're dealing with a Goliath/David crossover (e.g. X-Files/anything-not-listed-on-the-front-page) where too much exposition of Goliath will make Goliath's fans get bored. In a case like this, your best bet is to play to Goliath's fans; if need be, you can put a primer for David's fans next to the disclaimer so that they're not totally lost.
Don't forget, from a missionary standpoint, that the purpose of a crossover is to sell fans of one fandom on another fandom.