Well, I usually have a 'main pairing' (and won't usually like the original series unless the main pairing is the most plausible pairing, IMO, at the end of the story) and sub-pairings are unimportant. I do have preferences in the sub pairings, but I'll read fanfics without them\contrary to them, provided the main pairing is present. If the fanfic goes contrary to the main pairing (doesn't have to be present, but can't be ruined, in other words), I won't read it.
Main pairing always listed first.
Edited with a small addendum of other series. (and someone below says I'm the most serious person on this board? Huh? Hm... I didn't THINK I was the most serious person on this board...)
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Naruto:
NaruSaku (of course)
ShikaTem
ShikaIno
KibaHina
LeeTen
NejiTen
Fourth\Anko (heh)
UndeadFourth\Ino (double heh)
Ranma:
RanAkane
KunoNabiki
RyougaAkari
RyougaUkyou
ShampooMousse
Full Metal Panic
SousukeChidori
MaoKurz
Oh! My Goddess
BellKeichi
UrdPeorth (I think this is the most crack pairing I have outside of Undead4thIno in Naruto)
(I have pairings for both Skuld and Hasegawa, as well, but I can't remember the other character's names -- just faces)
Patlabor
NoaAsuma
GotohShinobu
KumagamiWong
KanukaHer late fiance in NY (manga only char, and I mean before he died)
Kimagure Orange Road
MadokaKyousuke
HikaruYuusuke
The Kasuga Sisters\Hatta and Komatsu (interchangable)
Fushigi Yuugi
TamahomeMiaka (note: I hate the OAVs and will never watch them again. And I will never read a Miaka\anyone else fic after seeing the ending of the TV series -- god, talk about ruining a happy ending)
Kenshin
KenshinKaoru
SanoMeg
YahikoTsubame
(I used to like AoshiMisao... but at the time I was really into Kenshin, there were a hundred AM fics for every one other fic in another pairing. It's like yaoi in Naruto fanfiction -- too many fangirl squeeling fics, so I have a hard time enjoying it)
Slayers
LinaGourry
ZelAmelia
FiliaXelloss (provided Xelloss has enough retcon backstory to make it possible. Impossible, literally, in canon)
LunaXelloss (see above)
Irresponsible Captain Tylor
TylorYuriko
YamamotoShiaHas
DomAzalyn
(and the other pairings that make the novel Irresponsible Kids work, although I forget what they are. DomAzalyn, sadly, is still stalemated as of IK, but I still like the pairing...)
DBZ
GohanVidel
(very mild BraGoten, but I'm so anti-DBGT I barely consider Bra a canon character)
Bastard!!
DarshYoko
DarshArshes (my view is encompassed, really, in my fanfic 'Voluntary Imprisonment.' Yoko is the one he'll have kids with, but she's mortal, and largely appeals to his 'Rushe' persona. Arshes is the one he'll stay with for the rest of eternity, and appeals to his 'Dark Snieder' persona. Any other girls are... um, forgettable whims)
Inu Yasha
InuKagome
MirokuSango
Gargoyles
GoliathElisa
XanatosFox
MacbethGrouac (sp?)
DemonaMacBeth
AngelaBrooklyn (I know WHY this isn't the canon pairing, but I don't like it)
Voltron (DVD release finally announced)
KiethAllura
KoranNanny
LisaJeff
CrikCinda
GingerOrgy (she's seen flirting with Cliff, Hawkins, and -- in the crossover episode -- Lance. She's also the only girl whose attachments don't quite seem so certain in both series (KeithAllura is ostensibly canon -- moreso in the Japanese version, the comics, and V3D then in the toned-down original Voltron dub, as is LisaJeff and CrikCinda, but Ginger's left unattached on a ship full of boys, flirting with several of them... and still decides to make eyes at Lance. Hm...))
Teen Titans
RobStar
BBRav
BBTerra
Lois and Clark
LoisClark
JimmyLucy
JackCat (yay season 1 only characters!)
MaysonDan
Jonny Quest (TRA edition)
JonnyJessie
HadjiKefira(Go read the collected works of Debbie Kluge. Yeah, okay, she's the ONLY good fic writer in the entire fandom, but she's damned good. So good many others in the fandom consider Kefira, her original character, canon. Myself included -- the Jealousy Universe she's created is a BTC (better then canon) fanfic. Better yet, it can be read with little or no knowledge of the original series... which is good, since the original series is long gone and not available on DVD)
Princess Mononoke:
SanAkittenaka
Chrono Trigger
ChronoMarle
LuccaFrog
Young Wizards
NitaKit
I also have favorite pairings in the following series, but embarrasingly can't remember the characters' names enough to confidently list them:
You're Under Arrest
Ushio & Tora
3X3 Eyes
Yu Yu Hakusho
Kodocha
Trigun
Nadia
Vandread
Maison Ikkoku
And... unless I want to start getting into the really obscure things like Akazukin no Cha Cha, I think I'd better stop there.
Um, yeah. Guess I've got a few favs, huh?