This is going to be long, but after years and years of reading fics, I've built up a wealth of opinions that I need to let out. This is as a good a place to do it as any, I suppose. I'm sure some will disagree with some of these, but as I said, these are only opinions.
Therefore, TFF...I present these ten commandments for your inspection (or ten things that happen in fanfiction that really get on my nerves):
I
Thou shalt finish what thou starts
'nuff said. It's just frustrating to no end for fics to just die, leaving all of the plot lines twisting in the wind. Such frustration is often compounded when the author in question starts a new fic and practically abandons the previous one. It's not at all uncommon for authors to have dozens of fics in their name, but only a handful (or none at all!) complete. Not to name names or anything...because you know exactly who you are.
II
Thou shalt not murder the queen's English
or whatever language you happen to be writing in. I'll assume that's English. This means several things: First, grammar and spelling count. If the plot is really good, you might be able to get away with screwing those up, but don't count on it. For the love of all that is holy, keep your tense consistent. Pick one of either present or past and stick with it. On second thought, don't even mess with present tense unless you really know what you're doing. Next, avoid using foreign words in the general dialog and narrative. Things like proper names, titles, honorifics and words and phrases that have no exact English equivalent are OK, but stuff like, "yes," "no," "excuse me," "sorry," "hello," etc...are inexcusable. In certain fics, this could get complicated (i.e. if several characters are multilingual), so use you're best judgment. Rule of thumb: If you can use an English word to convey the same thought, then do it.
III
Thou shalt contemplate the consequences of thy actions
Seriously, plan, plan, plan. Don't just write without a purpose and no idea where the story is going. Only a select few can pull that off, and if you happen to be one of them, you should seriously consider writing professionally. For the rest of you, have a plan, an outline, something to help guide you. If you just go willy nilly into the night, chances are you'll either write yourself into a corner from which there is no escape, or worse, do something that completely and unequivocally derails your story. Plot twists are fun, but they can be extremely volatile if handled poorly. Trust me, I've seen stories that were absolute joys to read go right down the crapper in the span of a paragraph (kind of spectacular, actually...in a train wreck sort of way). Sure, recovery is possible, but by then, you've probably lost most of your readers.
IV
Thou shalt construct chapters of adequate length
Picture this: It's a lazy Sunday afternoon. Looking for something to pass the time, you peruse through your favorite fanfic archive. Finally a story catches you're eye. It seems interesting, the author appears to have a grasp on the English language, and best of all, it's nice and long at over 20 chapters. So you sit back, grab a snack, and jump in, expecting to be entertained for at least a few hours...only to find that each chapter is barely half a page a long...and it takes a grand total of fifteen minutes to get through the whole thing. Now you're bored again, AND you have a half eaten bowl of popcorn that's going to get cold while you search for another fic to read. Please, don't let this happen to your readers. You can reduce the chances of this happening if you actually take the time to plan out your story into appropriately sized pieces (see item III, above).
V
Thou shalt be intimately familiar with relevant canon
Because you can bet that your readers are. They'll notice every continuity error you make. What's that you say? Alternate Universe? Divergence? Doesn't matter. You need to know exactly how you're changing things in order to figure out exactly how those changes effect the universe you're writing in. It makes for a much better story if you do. If it's been awhile (or, if you've never done it at all), read or watch all relevant material available before any major undertaking. I realize that for longer series, this is highly impractical, but a good skimming of the important parts would do a world of good.
VI
Thou shalt be true to thy characters
Obviously, this goes hand in hand with item V. Characters have established personalities. When they do things that violate that personality, it seriously degrades the plot. Note that this also applies to characters of your own creation. Yes, we all want the protagonist to get down on one knee and proclaim his everlasting love for the lead female, but you can't just have him do it right then and there. Such a thing would be highly unsatisfying. You have to set up the scenario and carefully construct the circumstances to where one could honestly believe that that guy could bring himself to do (or say) such a thing. In other words, you need to plan ahead (see item III again).
VII
Thou shalt not cast Mary Sue
If you don't know who Mary Sue is, look her up. Google and Wikipedia are your friends. See to it that she never stains your fanfics. If you're new at writing, it's probably best that you avoid original characters altogether, but if you must, then tread carefully. It may be of use to plan (there's that word again...item III) in advance what specific roles your original characters will have in your story. That way, you can determine their base profiles and personalities before they get out of hand.
VIII
Thou shalt not permit subplots to hijack thy story
All too often, a story will be rolling along nicely, until a certain story arc comes along, or some subplot is introduced. The author takes some time to develop these, as all good authors should, but then something happens. The author spends a little too much time focusing on these subplots, and eventually what was once a subplot or a simple side story becomes the main story, and the original premise (the reason we started reading your fic in the first place) is relegated to the background. Don't let this happen. Plan (item III...starting to see a theme here?) out your plot lines in order to avoid this.
IX
Thou shalt not break into song and dance
This one's a little tough to explain. Fanfiction is a written medium. As such, there are certain things that you can do that you can not do in, say, and animated medium. For example, in a written medium, you can go into great descriptive detail. Animation, however, lacks a narrative, making such endeavors nigh impossible. Instead, you'll have to convey your meaning through visuals, actions, and dialog. Likewise, there are certain things that work in a visual medium (like Anime), that don't work in a written medium, such as background music (song), and sight gags (dance). If you try to insert such elements into your written story, they will fail, because they are meant to stimulate sight and sound, something that is impossible to do in written form. Basically, they wind up being huge distractions that adversely affect the flow of the story. Also, take care with action sequences (especially fight scenes). We want to know what's going on, but don't go into painstaking detail, otherwise you'll wind up slowing the pace of the story down (action sequences are supposed to be fast paced). Tell us the important parts; our imaginations will fill in the rest.
X
Thou shalt not employ inappropriate literary risk
Finally, it should be understood that breaking the rules (even these rules) is OK, provided that you know that you're breaking them, how you're breaking them, why you're breaking them, and it is obvious to the reader why you're breaking them. This is what is known as literary or compositional risk. If you are unfamiliar with the concept or risk, I suggest that you learn it, as it can be a powerful tool in the hands of a skilled author.
