Please, nobody think less of me for this. But, I've threatened to make this thread multiple times now and have gotten some support from authors and commenters alike, so I've decided that it's probably time I put this up for everyone to see.
Fan-fic is a pretty funny thing. With normal writing, people actually purchase books to read them, and we can all agree that that's cool, and once you've paid your cash the author in question has no right to ask any more from you. But fan-fiction is quite different, I'm afraid. Fan-fics are works of love, works of practice, and sometimes works of fun, but they do all require work and effort, and the only reward that the authors in question can expect is for someone to read their story, and tell them what they thought.
A lot of people, however, will read the whole bloody thing, regardless of how long it is, enjoy it or not, and then just... move on. This is pretty uncool.
Slightly better is when people read the whole thing, then take a quarter of a second to splatter their fingers across the keyboard enough to say "pretty cool" or "nice job", or "was okay."
In a slightly different category is when people decide that the author needs their help; perhaps the story has some flaws. So they tear into the story, ripping it apart savagely and bringing the author to their knees before them where they lash at them with the Scourge of Shame. Now, I understand the desire to do this -- most authors ask for constructive criticism. The problem is when "constructive criticism" becomes "destructive criticism".
So far I've mentioned how NOT to comment. I'm getting to the how to comment part now.
Once you've read a story, it doesn't take you long to say what you liked about it, and what you didn't like. You have two options to create a really great comment which can easily be the size of two sentences or so, and take about a minute of your time, dramatically less time than it took you to actually read the story in the first place.
#1: Say a few specific things you liked about the story. Pick out a few lines that tickled you, comment on the wordplay or writing, or specific pieces you enjoy ("I love how that one girl keeps doing those sound effect things!" or whatever). Maybe pick out a part of writing, such as the dialogue or characters, and tell the author how you feel about it. This will make the author feel satisfied and happy with themselves, and your comment will not have gone in vain. Just saying "good job" will garner a reaction from the author of equal enthusiasm -- not much.
#2: Destroy, and build. This is if you really want to get inclusive. Start by saying the story has its high and low points, if it indeed does. This will make the author not feel attacked. They wrote this thing, and to have it destroyed before them will not leave them very open to criticism. What's that, you say? They asked for criticism? Well, maybe they did, but they lied. They want NICE criticism and, believe it or not, that's really not much of a challenge.
Tell the parts of the story that you disliked, and some suggestions on how the author can fix them. This can be done GENTLY, it's not all that hard, and gentler criticism has a much greater chance of making a lasting change in the author's writing. Once you've said what you don't like, refresh and invigorate them by doing #1 -- EVEN IF YOU HAVE TO LIE. Pick out SOMETHING good, even if it's just the idea. If it's completely awful, tell the author that it has potential, and that practice makes perfect! These are still true, and they'll leave the author (hopefully) ready to improve their game with the advice you've given.
I hope some of you read this, and I hope that it makes some small difference in the way that this site comments on the fan-fics that get churned through here day by day. By doing your part, you can bolster the confidence and skills of our writers, and give them the motivation to keep doing what they do. What's the worst that can happen, you give your fingers some exercise and lose two minutes of your time?