Alex and Marissa in the second season of the O.C. when their on the beach.

Willow & Tara's kiss (Buffy, Season 6) in the episode Entropy. Beautiful!

You probably have it already but the Angel-Collins kiss from "I'll Cover You".

Oh you know I have that one, Sarah. And Buffy I got.

I figured as much, lol. I think there is one from House MD between Thirteen and some random chick but that was a one-night-stand.

It was Thirteen and Spencer

megan and graham from but im a cheerleader
linda and amy from if these walls could talk(TV)
luce and rachel from imagine me and you
brandon and lana from boys dont cry

u also have a lot of moments in the l word

oh, i forgot, libby and sophie from carnivale(TV)

Has anyone else noticed that these are all lesbian kisses (with the exception of Collins and Angel)?

LOL!

I'm compiling my clips now, taking your suggestions to heart, and finding some gay men too. The video might be up within the week. I'll dedicate it to you fine folks. Are you excited?

Clips I have:

Angela and Roxie (Bones)
Thirteen and Spencer (House)
Xena and Gabrielle (Xena)
Willow and Tara (Buffy)
Maureen and Joanne (Rent)
Bette and Tina (L Word)
Lara and Dana (L Word)
Alex and Marissa (The OC)
Luce and Rachel (Imagine Me And You)
Angel and Collins (Rent)
Brian and Justin (Queer as Folk)
Zach and Shaun (Shelter)
Jack and Jack (Torchwood)
Jack and Ianto (Torchwood)
Louis and Prior (Angels in America)
Scott and Harvey (Milk)
Ennis and Jack (Brokeback Mountain)

Any other recommendations?

Scotty and Kevin (Brothers and sisters)

How about Scarlett and Penelope kissing in Vicky Christina Barcelona?

Uhm this is a favourite of mine:
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Sue/Maud - Fingersmith.

Isn't there somewhere where Jack kisses The Doctor, I think at the end of Series 1 (so 9th Doctor)? I know they aren't technically a couple, but you know Jack is in love with The Doctor forever.

Though I'm sure you've done this video already, so it doesn't matter.

Jack kissed the Doctor in season one finale. I don't know if it was 'Bad Wolf' or 'The Parting of the Ways' ;)
But I love Jack from this moment on :D

You definitely need a bit of Naomi and Emily in there from skins =D
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L Word season 2 episode 5 - Dana and Alice's first time. It is the perfect balance of hilarity mixed with hawtness. God they were the best couple on that show!