Birds Of Prey: In the tv-series, Barbara/Helena. The show itself might have sucked, but I enjoyed their friendship a lot. In the comics, Barbara/Dinah, who have probably the closest thing to buddy cop-dynamic that I've seen in f/f-relationships.

Bones: I second the Brennan/Angela-friendship above. I love how wonderful and functional their friendship is, although they're so different from each other.

BTVS: Buffy/Willow-bff-ness in the early seasons was like candy for me. I also wish the show would have done more with the Buffy/Tara-relationship, because the moments they connected were very wonderful.

Deadwood: Alma/Trixie. Again, a functional friendship between two very different women. Their relationship was always something I would have loved to see more of in the show.

Firefly: Inara/Kaylee, and also Kaylee/River.

Grey's Anatomy: Christina/Meredith. I don't always like Meredith, nor do I like the show itself much anymore, but I've loved the Christina/Meredith-friendship from day one.

Smallville: Chloe/Lois. Their relationship has become more complicated in the seventh season, but I love how obvious it is that these two care so much for each other.

Veronica Mars: Veronica/Mac. A wonderful, fun dynamic that never got enough attention in the show.