HARRY POTTER

What are you Worth by Kati-chan
Fenrir/Harry
http://hp.adultfanfiction.net/story.php?no=600017207

Onyx Snow by Kamerreon
Harry Potter/Blaise
http://www.fanfiction.net/s/4499083/1/Onyx_Snow

Faeritayle by Kamerreon
Harry/Harry
http://www.fanfiction.net/s/4785089/1/Faerietayle

Call of the Wild by Bittersweet Alias
Harry/Remus
http://www.fanfiction.net/s/4465491/1/Call_of_the_Wild

Incorrigible Infatuation by Bittersweet Alias
Marcus Flint/Harry Potter
http://www.fanfiction.net/s/4746794/1/Incorrigible_Infatuation

Nicodemus by Desolate03
Harry/Draco Lucius/Severus Neville/Blaise Ron/Voldermort
http://www.fanfiction.net/s/4088595/1/Nicodemus

Radix Acclaro by Random Dispatcher
Harry/Lucius/Voldermort Hermoine/Draco/Severus
http://www.fanfiction.net/s/2479661/1/Radix_Acclaro


HARRY POTTER XOVERS

Mirror, Mirror by Scyllablue
[HP /BTVS]
Angel/Riley Wesley/Spike/Xander
http://www.squidge.org/peja/cgi-bin/viewstory.php?action=printable&textsize=0&sid=31641&chapter=all

Hurt and Comfort by MultiMapper
[ON GEOCITIES]
[Buffy x X-men x Star Trek: Voyager x Superman x Dark Shadows x Due South]
Andrew/Scott Xander/Remmy
http://www.geocities.com/multimapper/hurt/hurtmain.htm

BTVS

Breathing by Rote by Scyllablue
Angel/Riley Spike/Xander
http://www.squidge.org/peja/cgi-bin/viewstory.php?sid=16516

Beginnings by MultiMapper
[ON GEOCITIES]
Xander/Wesley
http://www.geocities.com/multimapper/begins/beginsmain.htm

A Matter of Series by Kay
Angel/Doyle/Spike/Xander
http://ssfdu.tripod.com/kay/kaybtvs.htm

INUYASHA

The Wolf and The Dog by Miyuki M
Inuyasha/Koga
http://www.fanfiction.net/s/2247409/1/The_Wolf_and_The_Dog

Ever After Sequel to The Wolf and The Dog by Miyuki M
Sesshomaru/Miroku
http://www.fanfiction.net/s/2400566/1/Ever_After

Lost Hope by Miyuki M
Inuyasha/Koga
http://www.fanfiction.net/s/2399012/1/Lost_Hopes

The Prophecy by Mshutts
Inuyasha/Sessomaru
http://www.fanfiction.net/s/2748723/1/The_Prophecy

MISC.

Unexpected Comfort by Kay
Ardeth/Jonathan
http://ssfdu.tripod.com/kay/unexpected.htm

Come as You Are by DarkAngel1985
Hannibal/Will
http://movies.adultfanfiction.net/story.php?no=544210780

A Winter Tale by DarkAngel1985
Ichibod/Horseman
http://movies.adultfanfiction.net/story.php?no=544216707

Mist by Reigning Fyre
Sokka/Zuko
http://www.fanfiction.net/s/2691736/1/Mist

Reunion by aichakuMEC
Zim/Dib
http://www.fanfiction.net/s/3705813/1/Reunion

Sexual Frustration by Tesgura
Vlad/Danny
http://cartoon.adultfanfiction.net/story.php?no=600040153

Death and the Goblin by Hamilcar
Harry/Peter
http://www.fanfiction.net/s/3528635/1/Death_and_the_Goblin

Always Want You by Hamilcar
NightOwl/Rorschach
http://www.fanfiction.net/s/5048601/1/Always_Want_You

Kiss from a Rose by SOrion
http://www.fanfiction.net/s/2789428/1/Kiss_from_a_Rose

The A Matter of Series has a Demon made Xander do it, story thread.
Reunioun has NonCon by a third party.
Lost hope has a Mating season made them do it story line.
Sexual Frustration has Noncon by one Main Character on another.

As far as I can remember all the finished stories end happily.

Hurt and Comfort is a Series of Stories the last two of which are WIP but you can read it quite happily without those two.

The Prophecy is a WIP but true love is conquering all.

Breathing by Rote is a WIP that might not be continued, but it's at a relatively good stopping point.

Strangely, while my favourite pairings are rarely the most popular ones in their fandoms, looking through my bookmarks I also have very few truly rare pairings there. It's not through lack of wanting them, though! Just hard to find long, good quality ones I suppose.

I do have 4 Giles/Cordelia (http://delicious.com/Lanta/giles%2Fcordelia) Buffy fics bookmarked. I have a strange love for that pairing. I think a couple of the fics are fairly long; the other two just ficlets.

I don't know enough about Alias fandom to know which pairings are most popular; how common is Sydney/Weiss? (When Stavros Met Sofia (http://chaos.horsechicks.com/stavrossofia.html), short but great fun.)

There's a Star Wars one that kind of fits... it's a rare pairing (Jaina/Wes) but the "pairing" is only there in terms of one character flirting with the other. Great fun although best appreciated by someone familiar with the EU and particularly Aaron Allston's "Enemy Lines" duo of novels. Those Rituals Pertaining to Courtship (http://www.fanfiction.net/s/2469608/1/Those_Rituals_Pertaining_To_Courtship).

Other than that, just some rare crossover pairings if those count:
An Equal Temper (http://carlyinrome.livejournal.com/336246.html) (Angel x Bones: Cordelia/Booth)
The Longest Three-Week Day (http://michelel72.livejournal.com/49511.html) (Doctor Who x Stargate Atlantis: Rodney/Donna)
Look But Don't (http://moodfic.livejournal.com/66649.html) (Buffy x X-Men: Rogue/Faith)

The Cripple Arc (http://velvet-mace.livejournal.com/66460.html) by Velvet Mace (FMA, Ed/Hohenheim; warnings for noncon and dubious consent.)
Happily Ever After (http://www.prillalar.com/fic/stories/000267.php) by Halrloprillalar (Stargate SG-1, Jack/Thor)
Those Big Dark Eyes (http://www.area52hkh.net/asa/ayarkona/deyes.php) by Am-Chau Yarkona (Stargate SG-1, Jack/Thor)
Practical (http://www.unfitforsociety.net/musesfool/practical.htm) by Victoria P. (Chronicles of Narnia, Peter/Susan)
clear sunny skies (on the morning of the apocalypse) (http://meretricula.livejournal.com/97769.html) by meretricula (Twilight (lol), Jacob/Leah and Jacob/Seth)
Someone Else's Memoirs (http://community.livejournal.com/pinkceptional/19911.html#cutid1) by radiocakes (Twilight, Jasper/Bella) <-- Seriously, read this.
Bowling for Kittens (http://blackmamba-esq.livejournal.com/9506.html) by blackmamba_esq (Ugly Betty, Wilhelmina/Daniel)
And then everyone (http://yuletidetreasure.org/archive/73/andthen.html) by teinte (Vinland Saga, Thorfinn/Canute)
Facades (http://www.fanfiction.net/s/156942/1/Facades) by Sean Gaffney (Slayers, Lina/Naga - well, technically it's gen, but there is subtext.)
Have Yourself A Fluffy Cluffy Buffy Christmas (http://beer-good-foamy.livejournal.com/2668.html) by beer_good_foamy (Buffy the Vampire Slayer, Buffy/surprise)
A Nice Guy, Romantic Crap, and Stifler (http://www.matthewtime.com/aniceguy.html) by Matthew Haldeman-Time (American Pie, Oz/Stifler)

I was surprised to find that no one's ever rec'd anything for Ranma ½. If I'd noticed I'd have mentioned Ill Met By Starlight (http://www.thekeep.org/~mike/imbs.html) during the previous topic and mentioned a couple of other stories that really shouldn't be overlooked. But since they all focus on canon pairings, have these instead:
Ranma and the Heart of the Phoenix (http://www.csus.edu/indiv/s/seifertv/toth/amaw-rhp.txt) by Vince Seifert (Ranma/Kiima)
Roses of Shadow (http://www.sterman.org/index.html) by Richard Lawson (Ranma/Kodachi)
The Veils Placed Over Others' Eyes (http://www.florestica.com/dbsommer/oneshot/tvpooe/index.htm) by D.B. Sommer (Nabiki/Ukyou, Akane/Mousse, Ranma/Ryouga, Ranma/Shampoo, Kasumi/Tofu, Cologne/other(s))

I might also have mentioned Bliss, a (mostly) Ranma/Kuno epic written by a couple of the amazing folks at Transpacific Fanfiction (http://www.thekeep.org/~mike/transp.html), but it seems to be offline right now. ;_;

I like this topic! It's always fun to try something a bit different.

HARRY POTTER
Dark Beauty
(Snape/Sir Cadogan) (yes, the portrait)
http://snapeff.quasi-evil.net/home/endfest2/archive/beauty.html

Re-Discovery
(Snape/Hagrid)
http://bethbethbeth.livejournal.com/65237.html

Night-blooming Heartsease
(Snape/Neville)
http://yearningvoid.net/stories/julad/000080.html
---
Watch out with this one; it might make you cry.


BATMAN
Everything he's not
(The Riddler/Harley Quinn)
http://community.livejournal.com/batfic_contest/51868.html

BUFFY
Let Us Never Speak Of This Again
(Buffy/Giles/Willow/Xander)
http://trkkr47.seeking-solace.com/fanfic/letusnever.html

DISCWORLD
Death Insurance
(Vetinari/Death)
http://yuletidetreasure.org/archive/34/deathinsurance.html

NARUTO
Definitely not a Love Story
(Guy/Kakashi)
http://manicjoy.livejournal.com/4523.html

FINDING NEMO
what it feels like
(grown-up!Nemo/Gill)
(12.000+ words!)
http://www.waxjism.org/cimorene/hp/whatitfeelslike.html

SGA/1
Untitled
(Teyla/Teal'c)
http://jmtorres.livejournal.com/766205.html

X-OVER: EDWARD SCISSORHANDS/X-MEN
Claws
(Wolverine/Edward Scissorhands)
http://ciceqi.slashcity.com/Claws.htm
---
Yes, that pairing is insane, but a very good kind of insane! The writing is terrific, the characterization perfect, and it's also strangely sweet. While containing knife-play! (Kinda? I don't know. It didn't feel like it.)


... Now that I think about it, I seem to have reinterpreted the request as crack!pairings.
-Indigo

One of my favourite rare pairs is in Criminal Minds:
Cara Mia, by innerslytherin and severity_softly
Penelope Garcia/David Rossi
It is a sweet, gentle romance. I really wish they would do more with this pairing.

~~~~~ ~ ~~~~~
And, I'm embarrassed to do it, but I'm going to throw one of mine your way. I won't be offended if you simply ignore this one, but you did say rare and I'm pretty sure you won't find much of this pairing anywhere out there.

X-Files/L&O:Criminal Intent
Inatteso Part 1 (http://tres-mechante.livejournal.com/48840.html), Part 2 (http://tres-mechante.livejournal.com/49005.html), and Part 3 (http://tres-mechante.livejournal.com/49392.html)
Fox Mulder/Bobby Goren
An unlikely romance between two alpha males. The plot is cliche: undercover at a relationship building weekend for gay couples. Goren has a little trouble relaxing into his role. Mulder has entirely too much fun embracing his role, especially since doing so yanks Goren's chain.

What? This was written as a dare. Apparently I'm incapable of turning down a writing dare. *headdesk* (http://community.livejournal.com/geekystudmuffin/18253.html)