To paraphrase Pirates of the Caribbean, the "shopping list" is more guidelines than actual rules. Plenty of really good, fleshed-out characters have characteristics of Mary-Sues, but they have things that balance them out. What makes the sort of Mary-Sue that people spork is when the character has nothing but Sue-ish characteristics.
I have no problem with moderate Sues in original fiction, as long as they're coupled with decent writing and an interesting story. However, it is good to know the rules before you go breaking them, so that you know your character's Sue-ish characteristics and can balance them out.
There are always stupid people who flame (give overly harsh reviews to) stories because they have nothing better to do. Usually, they have nothing worthwhile to say. Someone who is honestly concerned with the quality of your writing, and not just making you feel bad, will give you a well-rounded critique that points out flaws and strengths and doesn't just say, "OMG, thats a MarySue!"
In fanfic, the big concern about Sues is that they are often coupled with bad writing and/or mangling of canon. The stereotype of a Suethor in Lord of the Rings, for example, is a Legolas/Aragorn fangirl whose character exists only for living out her creator's romantic fantasies, and has bad grammar to boot. Because of this stereotype (which is not unfounded--many Suethors are like that), many readers start flaming the minute they see something that might be Sue-ish. It's unfair, to both authors and readers, but it seems to be an unavoidable part of the fanfic community.
Yeah, I've figured out the cliche Mary Sues in several fandoms: in the "Matrix" series, most Mary Sues are "OMG TEH REEL WUN!!1111", or "Neo's-twin-just-not-mentioned-in-the-movies-who-goes-out-and-kills-the-Merovingian-and-the-Machines", or some random girl who gets kidnapped by the Merovingian and becomes the Mercury Twins's girlfriend. In "Hellsing", she seems to be some random girl who gets rescued/turned into a vampire by Alucard and/or becomes his girlfriend, whereupon Integra and/or Seras get "SEW JELLUS!11111" over the new girl.
Canon Sues of either gender (males are usually called Gary Stu or Harry Stu) are just as possible. I've mentioned Laurell K. Hamillton's Merry Gentry, but Dan Brown's Robert Langdon is another candidate: he's so special, he even has a job teaching a course that doesn't exist in any known university, much less at Harvard University. As is Sophie Neveu in "The DaVinci Code"; she's such a Sue that I tend to refer to her as Marie-Suzette since she's French.
Mind you, I can take a well-written Sue, but if -- as in the case of fanfiction -- the story is fraught with bad spelling, bad grammar, blatantly obvious lack of research, horrible logic violations (as in the case of the Mary Sue that told her friend she was seven months pregnant with the baby of the Sue-thor's obvious favorite male character, and said friend asked Mary Sue why she didn't look pregnant; replies Mary Sue, "Oh, I had surgery so I wouldn't look fat."), and canon character bashing (case in point, all those "Matrix" Sues who kill the Merovingian just because the Sue-thor hates him), I feel obliged to get out the scythe and do a little reaping.
