Mine:
1. Damon/Elena (The Vampire Diaries)
2. Kurt/Blaine (Glee)
3. Brian/Justin (Queer As Folk)
4. Mark/Lexie (Grey’s Anatomy)
5. Barney/Robin (How I Met Your Mother)
6. Klaus/Caroline (The Vampire Diaries)
7. Tony/Ziva (NCIS)
8. Pacey/Joey (Dawson's Creek)
9. Chuck/Blair (Gossip Girl)
10. Sookie/Eric (True Blood)
11. Ross/Rachel (Friends)
12. Buffy/Spike (Buffy the Vampire Slayer)
13. Puck/Quinn (Glee)
14. Rachel/Finn (Glee)
15. Nate/Serena (Gossip Girl)
16. Castle/Kate (Castle)
17. Ezra/Aria (Pretty Little Liars)
18. Sawyer/Kate (Lost)
19. Brooke/Lucas (One Tree Hill)
20. Penny/Sheldon (The Big Bang Theory)

1. Brian & Justin (Queer As Folk)
2. Lee & Kara (Battlestar Galactica)
3. Logan & Veronica (Veronica Mars)
4. Doctor & Rose (Doctor Who)
5. John & Cameron (Terminator: The Sarah Connor Chronicles)
6. Pacey & Joey (Dawson's Creek)
7. Rory & Jess (Gilmore Girls)
8. Buffy & Spike (Buffy the Vampire Slayer)
9. Freddie & Effy (Skins)
10. Nancy & Andy (Weeds)
11. Chuck & Blair (Gossip Girl)
12. Simon & Alisha (Misfits)
13. Will & Alicia (The Good Wife)
14. Damon & Elena (The Vampire Diaries)
15. Eric & Sookie (True Blood)
16. Seth & Summer (The OC)
17. Barney & Robin (How I Met Your Mother)
18. Kate & Sawyer (Lost)
19. Jim & Pam (The Office)
20. Tim & Lyla (Friday Night Lights)

11-20 is hard.. I wasn't sure what order to put them in.

1. Tony and Ziva (NCIS)
2. Jack and Sam (Stargate SG-1)
3. Daniel and Vala (Stargate SG-1)
4. Sam and Andy (Rookie Blue)
5. Peter and Olivia (Fringe)
6. Mulder and Scully (The X Files)
7. Chuck and Sarah (Chuck)
8. Hardison and Parker (Leverage)
9. Shawn and Juliet (Psych)
10. Piper and Leo (Charmed)
11. Booth and Brennan (Bones)
12. Niles and Daphne (Frasier)
13. Charlie and Alex (Saving Hope)
14. John and Aeryn (Farscape)
15. Nikola and Helen (Sanctuary)
16. Robin/Barney (HIMYM)
17. Harvey and Donna (Suits)
18. Sam and Jules (Flashpoint)
19. Rodney and Jennifer (Stargate Atlantis)
20. Buffy and Angel (Buffy the Vampire Slayer)

The first 7 are in order, the rest are muddled depending on what I'm watching.

1) Sookie/Eric (True Blood)
2) Damon/Elena (TVD)
3) Zoe/Wade (Hart of Dixie)
4) Tyler/Caroline (TVD)
5) Rumple/Belle (OUAT)
6) Sheldon/Amy (Big Bang Theory)
7) Chuck/Blair and Dan/Serena (GG)
8) Tessa/Ryan and George/Dallas (Suburgatory)
9) Jenna/Matty (Awkward)
10) Barney/Robin (HIMYM)
11) Matthew/Mary (Downton Abbey)
12) Jackson/Lydia (Teen Wolf)
13) Finn/Rachel and Kurt/Blaine (Glee) **I don't watch this show anymore but I still ship these couples.
14) Felicity/Ben (Felicity)
15) Casey/Cappie and Calvin/Heath (Greek)
16) Carrie/Big and Miranda/Steve (Sex and the City)
17) Logan/Veronica (Veronica Mars)
18) Buffy/Angel and Buffy/Spike (Buffy the Vampire Slayer)
19) Pacey/Joey (Dawson's Creek)
20) Monica/Chandler and Ross/Rachel (Friends)

Honorable Mention: Eric/Donna (That 70s Show), Samantha/Todd (Samantha Who?), and JD/Elliot (Scrubs).

Except for the first 7 they aren't in order because when I'm watching something sometimes that couple moves up in the ranks. It depends on what I'm loving at that moment.

1.Pacey and Joey
2.Logan and Veronica
3.Spike and Buffy
4.Klaus and Caroline
5.Daniel and Emily
6.Guy and Marian
7.Tim and Lyla
8.Evan and Casey
9.Kai and Erica
10.Mark and Lexie
11.Holly J and Decklan
12.Serena and Nate
13.Phoebe and Cole
14.Thayer and Emma
15.Kelly and Dylan
16.Annie and Jeff
17.Ben and Felicity
18.Jenna and Matty
19.Peter and Olivia
20.Annie and Liam

{1} Lucas/Peyton {One Tree Hill}
{2} Sawyer/Juliet {Lost}
{3} Nathan/Haley {One Tree Hill}
{4} Neal/Sara {White Collar}
{5} Jack/Kate {Lost}
{6} Barney/Robin {How I Met Your Mother}
{7} Tyler/Caroline {The Vampire Diaries}
{8} Damon/Elena {The Vampire Diaries}
{9} Derek/Meredith {Grey's Anatomy}
{10} Mark/Addison {Grey's Anatomy}
{11} Chuck/Blair {Gossip Girl}
{12} Mark/Lexie {Grey's Anatomy}
{13} Jackson/April {Grey's Anatomy}
{14} Ryan/Marissa {The O.C.}
{15} Nate/Serena {Gossip Girl}
{16} Seth/Summer {The O.C.}
{17} Alex/Izzie {Grey's Anatomy}
{18} Stefan/Rebekah {The Vampire Diaries}
{19} Klaus/Caroline {The Vampire Diaries}
{20} Nick/Jess {New Girl}

1. Buffy & Angel (Buffy the Vampire Slayer)
2. Damon & Elena (The Vampire Diaries)
3. Rumpelstilstkin/Mr. Gold & Belle (Once Upon a Time)
4. Donna & Harvey (Suits)
5. Veronica & Logan (Veronica Mars)
6. Brooke & Lucas (One Tree Hill)
7. Marshall & Lily (How I Met Your Mother)
8. Brennan & Booth (Bones)
9.Rory & Logan (Gilmore Girls)
10. Dani & Nico (Necessary Roughness)
11. Klaus & Caroline (The Vampire Diaries)
12. Nathan & Haley (One Tree Hill)
13. Cole & Phoebe (Charmed)
14. Gabby & Carlos (Desperate Housewives)
15 Monica & Chandler (Friends)
16. Mark & Lexie (Grey’s Anatomy)
17. Sookie & Eric (True Blood)
18. Dean & Bela (Supernatural)
19.Blair & Chuck ( Gossip Girl)
20. Barney & Robin (How I Met Your Mother)

Lets see...

1. Spike + Buffy (Buffy the Vampire Slayer)
2. Logan + Veronica (Veronica Mars)
3. Damon + Elena (The Vampire Diaries)
4. Phoebe + Cole (Charmed)
5. Rory + Jess (Gilmore Girls)
6. Cook + Effy (Skins)
7. Barney + Robin (How I Met Your Mother)
8. Stefan + Katherine (The Vampire Diaries)
9. Mick + Coralene (Moonlight)
10. Belle + Rumple (Once Upon a Time)
11. Nolan + Emily (Revenge)
12. Zoe + Wade (Hart of Dixie)
13. Nick + Jess (New Girl)
14. Jesse + Rachel (Glee)
15. Penny + Sheldon (The Big Bang Theory)
16. Emma + Jefferson (Once Upon a Time)
17. Jackson + Allison (Teen Wolf)
18. Dean + Jo (Supernatural)
19. Peter + Lydia (Teen Wolf)
20. Nina + Ben (Reaper)

1. Stefan-Elena (TVD)
2. Jess-Rory (Gilmore Girls)
3. Serena-Nate (Gossip Girl)
4. Julie-Matt (FNL)
5. Diviya-Evan (Royal Pains)
6. Zoe-Wade (Hart of Dixie)
7. Stefan-Katherine (TVD)
8. Mattew-Mary (Downton Abbey)
9. Luke-Lorelai (Gilmore Girls)
10. Mike-Jenny (Suits)
11. Jack-Kate (Lost)
12. Stefan-Caroline (TVD)
13. Matt-Rebekah (TVD)
14. Donna-Harvey (Suits)
15. Derek-Karen (Smash)
16. Hannah-Wren (PLL)
17. Bonnie-Damon (TVD)
18. Styles-Lydia (Teen Wolf)
19. Klaus-Caroline (TVD)
20. Scofield-Tancredi (Prison Break)

1. Buffy/Angel (BtVS)
2. Doctor/Rose (Doctor Who)
3. Willow/Oz (BtVS)
4. Lee/Kara (BSG)
5. Tony/Ziva (NCIS)
6. Sheldon/Penny (TBBT)
7. Barney/Robin (HIMYM)
8. Rumpelstiltskin/Belle (Once upon a Time)
9. Juliet/Sawyer (LOST)
10. Merlin/Morgana (Merlin)
11. Sherlock/Molly (Sherlock)
12. Michael/Maria (Roswell)
13. Dean/Jo (Supernatural)
14. Benson/Stabler (SVU)
15. Lily/Marshall (HIMYM)
16. Phoebe/Cole (Charmed)
17. Joan/Ryan Hunter (Joan of Arcadia)
18. Angela/Hodgins (Bones)
19. Shawn/Juliet (Psych)
20. Luke/Lorelai (Gilmore Girls)

The first two are actually tied, but after that it's no specific order. Like amshafe said, depends on what I'm watching/loving at the moment.

1. Damon & Elena (TVD)
2. Klaus & Caroline (TVD)
3.Monica & Chandler (Friends)
4.Kate & Baze (Life Unexpected)
5.Barney & Robin (HIMYM)
6.Veronica & Logan (Veronica Mars)
7.Ross & Rachel (Friends)
8.Aria & Ezra (PLL)
9.House & Cuddy ( House)
10.Nate & Jenny (Gossip Girl)
11.Matt & Rebekah (TVD)
12.Alaric & Jenna (TVD)
13.Lux & Sam ( Life Unexpected)
14.Penny & Sheldon (The Big Bang Theory)
15.Spencer & Wren (PLL)
16.Dan & Blair (Gossip Girl)
17.Caleb & Hanna (PLL)
18. Nate & Serena ( Gossip Girl)
19.Lilly & Marshall (HIMYM)
20.Alaric & Meredith (TVD)

I'll give it a shot...they might not be in exact order but here goes-

1.Rumplestiltskin and Belle (Once Upon a Time)
2.Dean and Castiel (Supernatural)...I don't care that they aren't canon, I'm still putting them
3.Jack and Ianto (Torchwood)
4.Marian and Robin (Robin Hood)
5.Barney and Robin (HIMYM)
6.Sookie and Eric (True Blood...but more so in the books)
7.Vic and Val (What I Like About You)
8.Monica and Chandler (Friends)
9.Emily and Nolan (Revenge)...once again not canon...but once again I don't care
10.Buffy and Spike (Buffy)
11.Abby and Connor (Primeval)
12.Jackie and Hyde (That 70's Show)
13.Sabrina and Harvey (Sabrina)
14.Sonny and Carly (General Hospital)...don't even watch this anymore but will never abandon this ship
15.Sheridan and Luis (Passions) Why the f**k didn't they end up together?!
16.Leela and Fry (Futurama)
17.Emma and Jefferson (Once Upon a Time)...actually I kind of OT3 them with Regina :)
18.Fran and Max (The Nanny)
19.Sheldon and Amy (Big Bang Theory)
20.Cory and Topanga (Boy Meets World)

I know I'm probably forgetting some couple I adore or something...but I managed to list 20!