my faves (in alphabetical order where possible):

(bold = faves within a fandom/category, bold purple = faves overall)

Alias/Stargate: 
couples: Sydney/John

Angel/Charmed:
couples: Cordelia/Wyatt, Prue/Angel, Phoebe/Spike

Angel/Mutant X:
couples: Gwen/Brennan, Faith/Jesse, Faith/Brennan

Angel/Human Target:  
couples: Fred/Chance, Faith/Chance

Angel/Stargate: 
couples: Fred/Lorne, Fred/John

Angel/Supernatural:  
couples: Illyria/Castiel, Fred/Sam, Fred/Dean

Angela's Eyes/Lie to Me

Animorphs/Primeval: 
couples: Rachel/Stephen, Rachel/Becker

Animorphs/Stargate

Animorphs/Twilight:
couples: Rachel/Jacob

Anna und die Liebe/Dead like Me

Anna und die Liebe/Ghost Whisperer
friends: Anna/Melinda, Jonas/Melinda

Anna und die Liebe/Medium
friends: Anna/Allison, Jonas/Allison 

Army Wives/Stargate

Being Human/Charmed: 
couples: Phoebe/Mitchell

Being Human/Supernatural

Blood Ties/BtvS: 
couples: Faith/Henry, Buffy/Henry, Willow/Henry, Vicki/Angel, Coreen/Willow
friends: Angel/Henry, Faith/Vicki, Faith/Coreen, Buffy/Vicki, Coreen/Willow, Dawn/Coreen

Blood Ties/Charmed: 
couples: Henry/Paige, Henry/Prue, Henry/Phoebe
friends: Prue/Vicki, Paige/Coreen

Blood Ties/Torchwood:
couples: Jack/Henry  
friends: Jack/Henry, Gwen/Vicki

Blood Ties/Veronica Mars:   
couples: Veronica/Henry

Bones/BtvS:
couples: Buffy/Booth
friends/rivals: Booth/Angel

Boston Legal/Drop Dead Diva

BSG/BtvS:
couples: Faith/Lee
friends: Faith/Kara  

BSG/Stargate:
couples: Dee/Ford, Kara/John
friends: Lee/John, Elizabeth/Roslin, Cadman/Sharon

BtvS/Charmed:  
couples: Buffy/Wyatt, Cordelia/Wyatt, Billie/Riley, Prue/Angel, Dawn/Chris, Phoebe/Spike

BtvS/Criminal Minds: 
couples: Faith/Spencer, Buffy/Derek

BtvS/Dexter:  
couples: Faith/Dexter

BtvS & Angel/Doctor Who & Torchwood: 
couples: Faith/Jack, Buffy/Jack, Buffy/the Doctor, Willow/the Doctor, Willow/Jack, Buffy/Gwen, Rose/Riley, Martha/Riley, Sally Sparrow/Riley, Faith/the Doctor, Fred/the Doctor  friends: Faith/Martha, Faith/Rose, Buffy/Gwen, Buffy/Rose, Faith/the Doctor

BtvS/Harry Potter: 
couples: Faith/Sirius, Dawn/Harry, Willow/Remus
friends: Hermione/Willow, Ginny/Faith, Hermione/Faith

BtvS/Human Target:
couples: Faith/Chance

BtvS/Legend of the Seeker:
couples:  Cara/Willow, Kahlan/Angel, Faith/Cara, Cara/Tara, Buffy/Richard, Cara/Kennedy
friends: Faith/Kahlan, Faith/Cara

BtvS/Leverage:
couples: Faith/Eliot, Buffy/Eliot
family: Eliot/Lindsey

BtvS/Lost Girl: 
couples: Bo/Faith , Bo/Angel, Bo/Willow
friends: Bo/Faith, Kenzi/Dawn

BtvS/LotR:
couples: Buffy/Legolas

BtvS/Percy Jackson & the Olympians:
couples: Dawn/Percy

BtvS/Primeval:
couples: Faith/Becker, Buffy/Stephen

BtvS/Smallville: 
couples: Faith/Oliver, Buffy/Clark

BtvS/Stargate:
couples: Faith/Ronon, Faith/John Buffy/Cam

BtvS/Supernatural:
couples: Faith/Dean, Sam/Dawn, Buffy/Castiel, Jo/Xander, Buffy/Sam, Jo/Riley, Buffy/Dean
friends: Faith/Ruby, Buffy/Ruby, Willow/Ruby, Dawn/Jo, Castiel/the Doctor

BtvS/Southern Vampire Mysteries & True Blood:
couples: Buffy/Eric, Faith/Eric
friends: Buffy/Sookie, Faith/Jessica, Angel/Eric, Spike/Eric

BtvS/Tru Calling:  
friends: Faith/Tru(or maybe twins?), Buffy/Tru

BtvS/Twilight:
couples: Faith/Jacob, Buffy/Jacob, Dawn/Jacob

BtvS/Vampire Academy:
couples: Faith/Dimitri

BtvS/Vampire Diaries:
couples: Buffy/Damon, Faith/Damon, Buffy/Alaric, Katherine/Angelus, Katherine/Spike, Angelus/Katherine/Spike, Dawn/Jeremy, Caroline/Riley, Willow/Rebekah
friends: Bonnie/Willow, Bonnie/Tara, Darla/Katherine

Chaos/Covert Affairs:
couples: Annie/Billy, Annie/Michael

Charmed/Dresden Files: 
couples: Prue/Harry

Charmed/Harry Potter:
couples: Prue/Sirius, Piper/Remus

Charmed/Hawaii 5-0:  
couples: Prue/Steve

Charmed/LotR:  
couples: Prue/Legolas, Phoebe/Legolas, Phoebe/Haldir, Paige/Haldir, Phoebe/Eomer, Paige/Eomer, Paige/Legolas, Prue/Aragorn

Charmed/Stargate:
couples: Paige/Cameron, Prue/John, Phoebe/Daniel, Billie/Ronon

Charmed/Supernatural:
couples: Paige/Sam, Prue/Dean, Billie/Dean, Jo/Chris, Jo/Wyatt, Ruby/Wyatt 
friends: Jo/Billie, Chris/Wyatt/Dean/Sam

Chronicles of Narnia/Harry Potter:
couples: Ginny/Caspian

Chuck/Supernatural:
couples: Sarah/Dean

Chuck/White Collar
couples: Sarah/Neal

Close to Home/Leverage:
couples: Annabeth/Eliot

Cold Case/Criminal Minds:
couples: Lilly/Derek

Cold Case/Dexter:  
couples: Lilly/Dexter

Covert Affairs/Criminal Minds:
couples: Annie/Spencer

Covert Affairs/White Collar:
couples: Annie/Neal

Criminal Minds/CSI

Criminal Minds/Dexter

Criminal Minds/Harry Potter:
couples: Hermione/Spencer

Criminal Minds/Life:
couples: Dani/Derek

Criminal Minds/Stargate:  
friends: Eli/Spencer

CSI/Dexter:     
couples: Debra/Horatio, Sara/Dexter, Catherine/Dexter, Sofia/Dexter, Debra/Warrick      
friends (or enemies?): Dexter/Horatio, Dexter/Nick, Dexter/Greg

Dark Angel/Mutant X:
couples: Max/Brennan

Dark Angel/Supernatural:
couples: Max/Dean

Doctor Who/Dr. Quinn:
couples: Michaela/the Doctor  
friends: Michaela/the Doctor, Martha/Michaela

Doctor Who & Torchwood/Firefly:  
couples: Inara/Jack

Doctor Who/Fringe:
couples: 'Altlivia'/the Doctor, Sally Sparrow/Lincoln Lee

Doctor Who/Game of Thrones:
couples: Daenerys/the Doctor
friends: Daenerys/the Doctor

Doctor Who/Harry Potter:
couples: Hermione/the Doctor
friends: Luna/the Doctor, Hermione/the Doctor

Doctor Who & Torchwood/Highlander:
friends: Duncan/Jack

Doctor Who & Torchwood/Legend of the Seeker: 
couples: Cara/Jack, Jennsen/Mickey, the Doctor/Kahlan, Jack/Kahlan, Gwen/Richard, Rose/Richard, Cara/Tosh 
friends: Gwen/Kahlan, Rose/Kahlan, Cara/Gwen

Doctor Who & Torchwood/Lost Girl:
couples: Bo/Jack
friends: Bo/Gwen, Kenzi/the Doctor

Doctor Who/Moonlight:
couples: the Doctor/Beth

Doctor Who/Primeval:
couples: Rose/Stephen, Martha/Becker, Sally/Stephen, Amy/Stephen, Jess/Mickey

Doctor Who/BBC's Robin Hood: 
couples: Marian/the Doctor

Doctor Who/Secret Diary of a Callgirl:
couples: 10.5/Hannah, the Doctor/Hannah, Jack/Hannah, Jack/Belle 
friends: Hannah/Rose (or maybe twins?)

Doctor Who & Torchwood/Stargate: 
couples: Jenny/Eli, Martha/Eli, the Doctor/Elizabeth, Sally/Ford, TJ/Jack, the Doctor/Sam
friends: Jack/John, the Doctor/Rodney, the Doctor/Eli, Martha/TJ, Jack/Cam, the Doctor/Sam, the Doctor/Daniel

Doctor Who & Torchwood/Supernatural: 
couples: Rose/Sam, Amy/Dean, Martha/Dean, Rose/Dean, Ruby/Jack, Jo/Mickey, Jo/the Doctor

Doctor Who/Twilight: 
couples: Bella/the Doctor, Bella/Mickey, Rose/Jacob, Jenny/Jacob
friends: Bella/Rose, Bella/Martha

Doctor Who/Vampire Diaries:
friends: Caroline/the Doctor

Doctor Who/Veronica Mars: 
couples/friends: the Doctor/Veronica

Farscape/Stargate: 
couples: Sam/John, Vala/John, Aeryn/Cam
friends: Aeryn/Vala, Aeryn/Sam, Cam/John, John/John

Friday Night Lights/Gossip Girl:
couples: Blair/Tim

Friday Night Lights/One Tree Hill:
couples: Brooke/Tim

Fringe/Supernatural:
couples: Olivia/Dean
friends: Olivia/Sam, Peter/Dean/Sam

Game of Thrones/Legend of the Seeker

Game of Thrones/Lord of the Rings
couples: Daenerys/Legolas

Game of Thrones/Stargate
couples: Daenerys/Ronon

Gilmore Girls/Supernatural: 
couples: Rory/Sam

Harry Potter/Leged of the Seeker: 
couples: Cara/Severus, Kahlan/Sirius, Kahlan/Remus, Minerva/Zedd

Harry Potter/Percy Jackson & the Olympians: 
couples: Hermione/Percy
friends: Harry/Percy, Annabeth/Hermione

Harry Potter/Pretty Little Liars: 
couples: Aria/Harry

Harry Potter/Primeval:
couples: Ginny/Stephen

Harry Potter/Sky High: 
couples: Ginny/Warren, Layla/Harry

Harry Potter/Supernatural: 
couples: Hermione/Sam, Ginny/Dean
freinds: Dean/Sirius

Harry Potter/Twilight:
couples: Ginny/Jacob, Hermione/Jacob, Cho/Edward, Hermione/Edward
friends: Jacob/Sirius, Harry/Jacob, Hermione/Bella, Bella/Ginny

Haven/Supernatural:
couples: Audrey/Dean

Hawaii 5-0/Moonlight:
couples: Beth/Steve

Hawaii 5-0/Stargate:  
friends: Steve/John, Steve/Ronon

Hercules/Xena/Legend of the Seeker:
couples: Cara/Hercules, Kahlan/Hercules 
friends: Xena/Cara, Kahlan/Xena, Kahlan/Gabrielle, Richard/Hercules

Hercules/Percy Jackson & the Olympians/Xena:
friends: Percy/Hercules, Chiron/Hercules, Chiron/Xena

Hex/Supernatural:
couples: Cassie/Dean

Human Target/Leverage:
friends: Ames/Parker, Chance/Eliot

Human Target/Supernatural:   
couples: Emma/Sam, Ames/Dean  
friends: Dean/Christopher

JAG/Stargate:
couples: Mac/John, Mac/Jack
friends: Mac/Sam

Legend of the Seeker/Lord of the Rings:
couples: Kahlan/Legolas, Kahlan/Aragorn, Cara/Legolas 
friends: Arwen/Kahlan, Aragorn/Richard, Legolas/Richard, Richard/Gimli, Gandalf/Zedd

Legend of the Seeker/Prince of Persia:
couples: Kahlan/Dastan

Legend of the Seeker/Stargate: 
couples: John/Kahlan, Ronon/Cara, Cara/Cam, Teyla/Richard, Cadman/Richard, John/Cara, Kahlan/Cam, Jennsen/Ford

Legend of the Seeker/Supernatural: 
couples: Kahlan/Dean, Cara/Dean, Jennsen/Sam, Kahlan/Castiel

Legend of the Seeker/the L-Word: 
couples: Cara/Shane

Legend of the Seeker/True Blood:
couples: Cara/Eric

Leverage/Stargate:
friends: Eliot/Ronon

Leverage/Supernatural:
couples: Eliot/Jo

Leverage/White Collar:
couples: Parker/Neal
friends: Parker/Neal, Eliot/Neal, Hardison/Neal

Life/the L-Word:
couples: Dani/Shane

Lost/Stargate:
couples: Kate/John

Lost Girl/Stargate:
couples: Bo/John, Bo/Ronon, Bo/Cam, Kenzi/Ford

Lost Girl/Supernatural: 
couples: Bo/Dean

Lost Girl/True Blood:
couples: Bo/Eric, Bo/Alcide
friends: Bo/Sookie, Jessica/Kenzi

Moonlight/Veronica Mars:
couples: Veronica/Josef

NCIS/Stargate

Off the Map/Three Rivers:
couples: Ryan/Andy

One Tree Hill/Supernatural: 
couples: Brooke/Dean, Haley/Sam, Rachel/Dean

Primeval/Stargate:
couples: Cadman/Becker, Cadman/Stephen
friends: Becker/Ronon, Becker/John

Private Practice/Stargate:  
couples: Addison/John

Roswell/Smallville:
couples: Liz/Clark

Roswell/Supernatural:
couples: Liz/Sam, Maria/Dean

Sanctuary/Stargate: 
couples: Helen/Jack, Helen/Daniel
friends: Helen/Sam (or maybe family?)

Secret Diary of  a Callgirl/Supernatural:
couples: Hannah/Dean, Hannah/Sam, Dean/Belle

Secret Diary of a Callgirl/True Blood:   
couples: Belle/Eric
friends: Hannah/Sookie, Hannah/Jessica

Smallville/Supernatural: 
couples: Chloe/Sam, Chloe/Dean, Lana/Dean, Lana/Sam, Lois/Dean, Bela/Oliver, Jo/Oliver, Jo/Clark

Smallville/Twilight:
couples: Lana/Jacob

Stargate/Supernatural:
couples: TJ/Dean, TJ/Sam, Jo/Ford, Jo/Ronon, Vala/Dean, Anna/Eli
friends: Dean/John, Dean/Ronon

Supernatural/True Blood: 
friends: Dean/Eric

Supernatural/Vampire Diaries:
couples: Jo/Alaric, Jo/Damon, Elena/Sam, Elena/Dean, Caroline/Dean
friends: Katherine/Ruby

Supernatural/Veronica Mars:
couples: Veronica/Dean, Veronica/Sam

The Listener/True Blood:
couples: Sookie/Toby

Tru Calling/White Collar:
couples: Tru/Neal

True Blood/Vampire Diaries: 
couples: Jessica/Damon, Rebekah/Eric, Katherine/Eric, Caroline/Eric, Elena/Eric

Veronica Mars/White Collar:
couples: Veronica/Neal