I'd bang:
Morrigan (Dragon Age)
Shan Xi (Fear Effect)
Geralt (The Witcher)
Batman (Batman: Arkham Asylum)

Deadra. She was fun to look at. Unless you had a thing for Father/Mother, in which case, wtf?
Man, I love that game. Such an original and beautiful fantasy world.

Yeah her.
Dammit, I forgot to add Eya from Parasite Eve and Morrigan from DA: Origins.

Hmm... While I was playing a female character in Star Wars: Knights of the Old Republic 2, I kind of had a thing for Atton. What's odd about this is that I'm a guy, and that I normally don't have gender identity issues.
Also, Alyxx Vance.

It would also seem a good idea to include the game/series the character is from. For instance, when you say Morrigan, I think Darkstalkers and not DA:O.
My list of game characters I've had a crush on:
Annah and Fall From Grace - Planescape: Torment
Lara Croft - Tomb Raider series
Samus - Metroid series
Chun Li and Cammy - Street Fighter series
Konoko - Oni
Rayne - Bloodrayne
Therese and Jeanette - VtM: Bloodlines

The girl from Beyond Good and Evil
The girl from Heavy Rain
The girl from Tomb Raider
The girl from Broken Sword
The girl from Half-Life 2
The girl from Halo (that digital one)
Does it mean I'm a bad person if I only know what game they're from and don't remember their names?

Yes, because they are the most reminiscent names in vidya history.

I'm going to get a TON of weird looks for this one, but I'm just going to go with my first one, from when I was a little kid:
The nurse from Faxanadu.

You're bad for only including females.

No, that just makes you male.

Any character Jennifer Hale has voiced
April Ryan
Kane

Top 5:
1. Jade from Beyond Good and Evil;
2. The feisty girl from Mirror's Edge;
3. Maureen Corley from Full Throttle;
4. Alyx Vance from Half Life 2;
5. Chelsee from Under a Killing Moon

Viconia (BG)
Aribeth (NWN)
Neeshka (NWN2)
Scope (JA2)

Faith, or Celeste (Cel)?