Okay, if you don't randomly scroll my favorites list on FFnet, here are some really good works, separated by category.
Naruto:
Hopelessly, by Misato'sPenPen. Sasuke and Kakashi, M for good reason, yaoi.
Silver and the Sun, by max.tmy. Pairing undecided, but a wonderful AU by an author with a wonderful sense for people and their reactions. She's doing an excellent job, and every chapter released seems better than the last. I keep dying of laughter, but the story breathes new life into me all over again, so it works out.
12 Steps to Recovery, by SangoStar. Threesome, kinks, yaoi, KakashixItachixYamato. A wonderful take on addictions and treatment, if you ask me.
Broken to Domination, by FreedomFox. A brilliant AU-ish work with hot yaoi: ItachixKiba.
De Oppresso Liber, by Misato'sPenPen. A yaoi/incest AU with Sasuke, Itachi, and Kakashi. HOT.
Freeze Burn Tokyo, by Leilita Chan. NejixShika AU college fic. Hot, with tension.
Honey Blue Sky: Freeze Burn Tokyo SIDEFIC, by Leilita Chan. Takes a spin off the main plot of FBT to become KakashixShika. Hot, with angst.
Give and Take, by StarkBlack. Kakashi and Genma. Starts out as a no-strings-attached friends-with-benefits kind of thing, develops into more. Also has a threesome. One of the overall hottest I've read with these characters.
Hours, by Surreptitious Chi X. Incest, Gaara and Kankuro. So far no yaoi, but developing nicely even though Kankuro seems too crybaby-ish for my liking. Will likely be uber hot in future.
In Hot Water, by UchidaKarasu. MinatoxKakashi, a get-together fic. Sly and humorous, with a tad of what could be called exhibitionism.
I like it muchly.
Instinct and Reason, by Fruiitcup. KibaxShika, kinky, amusing, and hot.
Laughter Lines, by checkerbloom. Hilarious MinatoxKakashi fic, with angst and sweetness.
On a String: Freeze Burn Tokyo SIDEFIC, by Leilita Chan. This one is KankuroxKiba, and mm, she sure has a flair for writing these two!
Release, by Ookami Kasumi. KibaxShika, NOT a heat fic. Just some fun getting together.
Scars, by Serani. A wonderful fic, developing what I suspect will be a threesome.
Strike, by ladywinterfic. An amusing KakashixNaruto fic. Humorous, sweet, and smexy all in one.
Tokyo Majin:
Soft, by AkumaStrife. The hottest KyouichixTatsuma I've read to date.
Gundam Wing/AC:
Umbra, by Clara Barton. A wonderful urban fantasy, complete with hot yaoi threesome. ;D
Deviant, by Clara Barton. Inspired by X-Men, Smallville, Misfits, and Heroes. Will have hot yaoi, possibly yuri? and is wonderfully written. I am so enthused with this fic, but that is as it should be; I'm beta'ing it for her. ;D
Smoky Hills, by snowdragonct. A wonderful, complicated, long story that will eventually have hot yaoi lovin'. All in all, it's a brilliant twist for an AU fic, and her style with characters and their pasts is excellent. Hopefully she'll have that update she was talking about soon....
In My Master's Arms (and its sequel, In My Lover's Arms), by Jewel of Hell. Intricate story involving magic and mayhem, and eventual yaoi. AU series with twists.
Another, by E-mu saru. Has one hell of a plot, and is excellently thought out and written for someone who is an artist by trade. I very much admire this work, and Lix still makes me crack up.
A Very Dark Corner, by Clara Barton. AU mystery/romance, one that makes me laugh and 'ooh' and 'ahh' at the details.
Final Fantasy XII:
Learning to Share, by oblivion's pen. An amusing and smexy threesome. Basch, Balthier, and Vaan.
Fire Emblem:
Trust, by wolfofsummerbreeze. From Rekka no Ken (Blazing Sword/Burning Sword, however you want to translate it), depicting Matthew's realization about how and why his relationship with Jaffar has changed.
Final Fantasy X:
Wrong?, by darklight1601. A take on yaoi, homophobia, and the game itself that is wonderful, though dark fairly often. Also has humor, though. AuronxTidus.
Final Fantasy VIII:
Whispered Screams, by Angry Angel. AU. Dark. Twisted, but hot.
Final Fantasy VII:
Writ Deep, by A Darker Shade. Just...read it. It's lovely yaoi.
Sword and Sorcery, by Ne'er-Do-Well. AU, SephxVin, so far not many chapters but it's looking to be a drawn-out, involved, action-filled yaoi story.
I Must Be Insane (and its sequel, Nothing to Say) by anime fearie. Will eventually be TsengxReno, I think. Back story on Reno and how he joined the TURKs, continuing on from there. Peaches will never look the same....
Fractured, by Madisuzy and...I don't recall. But it's on Madisuzy's account. It's a wonderfully twisted VincentxTseng story, and will hopefully be continued sometime soon.
Cold, by Emery Board. A semi-dark RufusxReno, topped off with humor and smut. Love it.
Yeah, I have me some favorite stories alright.