Why Daphne Greengrass has been addressed - it's probably because she's such an open canvas, for better or worse. As for why "Ice Queen," my guess would actually be that a few of the more well-known fanworks involving her portray her that way. Sorta like how a really well-known fanfic can establish itself as nearly canonical in other places: a LotR fanfic posted here that involved Lindir would, presumably, use the characterization given him in Don't Panic! and Okay, NOW Panic, despite neither of those being canon, technically speaking.

Ron!Bashing is... I don't know, just irritating. But Dumbledore, you must admit, was written as a fairly manipulative character. Fandom just takes it up to eleven.

This is the first I've heard about that! That seems weird, and I wish I had a better answer other than "I don't know." Hope you find out soon!

I've read all of the books... but who's Daphne Greengrass?

I read a lot of the fanfictions that pair Harry with rarer girls like Daphne, there aren't that many compared to say, Hermione or Ginny pairings but compared to pretty much every other 'rare pair' it's probably got the biggest backing.

I agree with Karen DuLay in that one of the most appealing reasons to pair Harry and Daphne is that she's really a blank slate for writers. However there are other reasons for it, I believe, moving into the others things you've said.
By wanting to make Harry different and stand out compared to the canon fanfic writers want someone different to be his love interest, if its another Gryffindor it's hard to stay away from Hermione and Ron because he'll still be spending time with Gryffindors, unless something along the lines of Lords Quarters are used (or Harry is in a different house, but that's a whole different kettle of fish). If he's with a Ravenclaw (Cho or Luna are the only two I've really seen it with although there are plenty of other girls mentioned in Ravenclaw if they have been paired with Harry in a story it hardly ever gets finished), with Cho it seems to carry on as if they never broke up in OotP and Luna is already part of his friendship group from 5th year onwards really and so things don't change. Hufflepuff gives a few decent girls, but considering most of their reactions to him in the books (Chamber of Secrets and Goblet of Fire especially) combined with Harry's usual new persona in these stories (unforgiving of those who've betrayed him etc.) means they don't really work. Now the only house left is Slytherin, which is the least obvious choice (and most shows Harry 'breaking away' from his old life). Of the mentioned girls in Slytherin Pansy is generally a no (besides being with Draco for most of the books) Millicent is generally seen as a barinless, slightly ugly minion of Pansy's leaving (really) Tracy and Daphne, Tracy isn't actually mentioned in the books, whilst Daphne is, making her the more obvious choice.
There's also the fact that most writers (including me at one point) seem to want to prove that Slytherins aren't always evil (something that canon seems to leave out, unfairly one might add). by pairing Harry (the usual epitome of good) with a Slytherin means that along with any statement of "We're not evil we're neutral" or something similar gives the writer (and maybe the reader) some sort of relief.
Moving on from Daphne, Ron is seen as the weak link of the Golden Trio, the stupid one, the lazy one, the one who betrays Harry the most etc. etc. and in canon no matter what Ron's done Harry doesn't seem to care and immediately accepts him as a best friend again once the apology is through (Remember this isn't my view point). In Harmony fics Ron bashing gives Harry and Hermione a way to fall in love and in other fics it gives Hermione a way of seeing how evil Ron is and join Harry's side. Manipulative Dumbledore is easy, it's pretty much written all over Canon and most people love to extend that and make it worse. Whilst I do write a manipulative Dumbledore I don't bash him or make him evil, (I tried once and realized how wrong it was) He fulfills more of a supporting role, reduced to that because of his manipulations and plans, but still on the side of good. And there are a few fics that do that.
There are Hermione bashing fics about, normally more severe betrayal ones but there are a good number if you search hard enough.
Manipulative Draco? No, I hadn't thought of that, but then again it may not really fit his character. Manipulative Lucius? Now that sounds like a good idea.
Err, why not? I don't know. I've seen them named Monica and Wendell as well (after the names they 'adopted' after Hermione memory charmed them). But then I've also seen them have different names as well.

Well, I'll stop with the wall of text for now

Storme Hawk

I suspect one reason the Daphne/Harry pairing is popular is because we know so little about Daphne, and thus fanfic writers can essentially take a canon character and give her whatever traits they want. As for her Ice Queen nickname...it may be because she was a Slytherin?

I've no idea about Daphne Greengrass, having only ever seen passing mentions of her in fanfic. It might just be that people associate her strongly with Draco/the Slytherin creed, but know very little about her - therefore making her perfect for "development" by pairing her with the hero.

However, the Ron-bashing has some theories behind it. The most enduring one I've seen is that he's not "special" the way Harry and Hermione are; Harry is the Boy Who Lived, the hero, the central figure, and Hermione is brilliant, pretty (they're usually going off Emma Watson's looks) and confident. Therefore, Harry is better than Ron because he's special, and Ron is ordinary and only bickers with her and is piggish (remember how much he likes his food?) and clearly does not deserve such a paragon of womanhood as Hermione. Essentially, Harry is the bigger prize because he's the hero and therefore Hermione must only ever settle for the bigger prize. But because canon says she and Ron love each other, people have to bash Ron to make Harry actually look like the more suitable partner and force Hermione into his arms.

Manipulative!Dumbledore is generally a way for people who want Harry to do his own thing let him do it. It's true that there was a fair bit of manipulation going on in the series by our twinkly-eyed Headmaster to get everything ready for the ultimate elimination of Voldemort - but it was done with good intentions. A lot of ficwriters ignore that, or blow it out of proportion, or twist it to make Dumbledore Teh Evulz so that Harry will break free and go on his merry way, building up his own power base and challenging people to gain even more power. Basically, it's to give Harry a power trip, because that's exactly what modest, unassuming, loving Harry really wants. Yup.

Hermione's parents being named Dan and Emma is just a bit of fandom meta, I guess - "LOL, we'll name them after Harry and Hermione's actors, aren't we original and witty?" seems to be the idea.

My apologies for the slight Wall O'Text... I get verbose about the Potterverse.