Over the years I've tried to create a set of rules I always use when I critique. Rules I sometimes wish everyone would use when they read my stuff. Like all rules your millage may vary and you might not agree with them. These are my rules and I like them.
1.) Be nice.
2.) Don't call anything you read 'fan fiction' or say 'it reads like fan fiction' The truth is, everyone is inspired by something and they're trying to write what they love to read or watch. My Arwen series is full of Star Trek like stuff, it's a conscience chose, I wanted to write something like Star Trek but with my own twist and when someone said 'it reads like Star Trek fan fiction' I wanted to jump through the screen and slap the guy or girl I was so mad. So yeah, don't say it's like fan fiction, you can bring up how it's similar to something but really, isn't everything similar to something out there already?
3.) Pay attention to the story. Sometimes, when I see something I don't understand, I always write something like "Maybe I just missed it but I thought-" Sometimes the writer removes some piece of information when he's going through another draft. Sometimes he never explains something. Sometimes the reader just misses it.
4.) Talk about the story in front of you, not the story you wished they had told. Okay, this is one I break more often than not. The story isn't mine, it's the authors and I need to read what they have written, not what I wished I had written.
5.) If you don't have anything nice to say, don't say anything. I have mixed feelings about this one. I only really comment on stories I like and ignore those that I don't. If it doesn't hold any interest for me, then I won't give it 100% in the comments and that's not fair to the author. I have mixed feelings about it because I should tell the author how to improve the story, how to make it so I would like it, but sometimes a story is just too poorly written or has a subject matter I'm not interested in and I just go to the next one. I wonder how many people do this with my stories and if they do, I can't be mad cause I do the same thing.
6.) Limit your back and forth. What I mean is, sometimes the person you critique will have questions about what you said, sometimes they'll try to defend what they said, sometimes they'll say you have no idea what they're trying to say. In any case, if the conversation is going no where then leave it go, there's only so much you can say to try and help someone and sometimes you're wrong. It's the writers work not yours so maybe you would kill the entire crew of a starship to make thing interesting, maybe you won't. Whatever the case do your best then get out!
So, that's it. Like I said, I've broken a few of these and I'm sure I'll break them again and again. Some stories you just need to. When my stories go through the grinder I really hope for the best but expect the worst. I continue to learn how to deal with critiques of my work and I continue to work on making my own critiques as true and helpful as possible.