Towards a Unified Sue Theory
In the realm of fan fiction, it seems that almost everyone has an opinion on Mary Sues: on what they are, on how to identify one, and on why people write them. Most of those opinions focus on the obvious attributes of Mary Sues, such as their appearance and skills. However, there is no one set of such features which will cover every Mary Sue, making identification of Mary Sues and proof of Sue-ness difficult. The answer to this is not more complex checklists and more detailed questions but, rather, an examination of why Mary Sues exist in the first place and how they manifest their Sue-ness as a result.
If you look up information on Mary Sues in fan fiction, you will find a vast amount of material. You will find opinions ranging from mild amusement to spittle-spraying hatred. And most of all, you will find numerous defintions, some of them contradictory, as to just what a Mary Sue is in the first place. Many of those definitions consist of checklists of features that which are common to Mary Sues, such as having an unusual name, striking physical appearance, exceptional skills, etc. Some of these get enormously complicated. However, those features are in fact symptoms of a deeper problem.
A true Mary Sue is recognized, not by what she looks like, nor even by what she can do, but by what effects she has on the story. The truly distinguishing feature of a Mary Sue is that she becomes the entire frame of reference for the story. Canon characters, and even events themselves, are reduced to the status of supporting cast. Everything in the story happens in relationship to the Mary Sue. If a recurring villain appears, he's there because of the Mary Sue: hunting her, trying to recruit her, etc. If two canon characters are talking with each other, it is in some way prompted by, or relates to, the Mary Sue, perhaps speculating on her background or discussing her relationship to one of the canon characters. If characters are chatting about the weather, it is only so they can be interrupted by the Mary Sue or observe her doing something. The reader starts to get the feeling that all of the other characters freeze into statues when the Mary Sue leaves the scene and only begin to move again when she returns.
This effect on the story is, quite possibly, the primary reason for reader hostility towards Mary Sues. We read fan fiction in order to read more stories about our favorite characters and their world. If a Mary Sue is present, however, those characters become little more than props on the stage where the Mary Sue is acting out her own story. The anger comes from disappointed reader expectations. We expected a Hogan's Heroes story or a Star Trek story or whatever, and in the end we just got a Mary Sue story with some canon stage dressing. The characters we wanted to read about -- the familiar fictional people whose lives we wanted to drop in on -- aren't really there at all. We naturally feel like victims of bait and switch.
The "specialness" of the Mary Sue develops as an effect of this warped frame of reference, rather than being a cause of the warp. Since the writer sees no other way for the canon characters to be so totally focused on an ordinary person, and indeed there may be no plausible way, the Mary Sue is given special characteristics such as an exotic appearance. Since it would likewise not be reasonable that all the events of the story could center around an ordinary person, the Mary Sue cannot be ordinary; she needs super-powers, a dark secret, or something else to make her not just important but central to the story. Anything that would prevent the Mary Sue from being the focus of the story must be suppressed. This leads to things such as canon characters acting inexplicably stupid so that the Mary Sue can point out something that should be obvious to them, or failing in their usual specialties so that the Mary Sue can come to the rescue with her superior skills.
With this in mind, it becomes much easier to spot a Mary Sue, either in someone else's story or, with horror, in your own. The critical question is no longer "is this an avatar of the author?" or "is this character too perfect to be real?" but, rather, "does this character serve the story, or does the story serve this character?" When it is the latter -- when you see the warping taking place, the frame of reference becoming the Mary Sue, and the canon characters being reduced to a mere supporting role -- then you know you have a Mary Sue. Taking away the Sue-ish characteristics does not cure the problem; they're only there to justify the Mary Sue's status in the story. What needs to be done away with (aside from the Mary Sue itself) is the focus on that character to the exclusion of all else. Make her a guest star, but leave the stars of the story to do their jobs. Let the story work out the way it should. That's what the reader is reading it for.
The following web pages are other opinions on the cause, effect, and identification of Mary Sues.