So many possibilities, including some I've never heard or thought of before.
**DC Comics**
Supergirl/Wonder Woman
Supergirl/Batgirl
Harley Quinn/Poison Ivy (pretty much canon)
Harley Quinn/Batgirl
Catwoman/Batwoman
Catwoman/Batgirl
Vixen/Hawkgirl (Shayera Hal)
Vixen/Wonder Woman
Supergirl/Starfire, Supergirl/Raven, or Supergirl/Starfire/Raven
**Marvel Comics**
Captain/Ms. Marvel and Black Widow
X-23/Jubilee (I like that idea)
Jean Grey/Emma Frost (That one, too),Jean Grey/Psylocke, or Emma Frost/Psylocke
Jean Grey/Shadowcat
Magma/Wolfsbane
Shadowcat/Wolfsbane
Captain/Ms. Marvel and Rogue
Storm/Jean Grey
Storm/She-Hulk
**Video Games**
FemShep and Jack/Kelly/Liara/Shiala/Ashley/Samantha/Miranda... Basically, any major female character, more or less. Also, FemShep and two other women, particularly Jack and Miranda. (Mass Effect)
FemWarden/Lelianna (Hardened)/Morrigan (Dragon Age: Origins)
Lara Croft/Rayne (Tomb Raider/Bloodrayne, although I've never played the latter)
Lara Croft/Sam (Tomb Raider, the most recent one)
**Other/Crossovers**
Selene and Violet (Underworld/Ultraviolet), or Selene and Alice (Underworld/Resident Evil)
Alice and K-Mart (Resident Evil film series)
Snow White/Maleficent (Snow White and the Huntsman and Maleficent the film, despite not having seen either), or Queen Ravenna/Maleficent (same, because Charlize Theron and Angelina Jolie, yes please!)
Carly/Victoria (iCarly/Victorious, but with them in their twenties, natch)
AJ Lee/Alicia Fox, AJ Lee/Paige... Lots of potentials (WWE, because it's technically a TV series, so...)
Merida/Astrid (Brave/How To Train Your Dragon)
I will probably add more as I think of them.