Candida Doyle plays/played keyboards with Pulp.
John Mellencamp’s band has a female violinist.
Ruyter Suys, guitarist for Nashville Pussy, is currently the only woman in the band, and is a guitarist.
Kim Deal was the lone female in The Pixies. Her sister Kelley was the lone female in The Last Hard Men. Both were primarily guitarists for these.
Kim Deal was the bassist for the Pixies, although the bass can be qualified as a type of guitar, if you’re being technical.
Laura Stein played (plays?) keyboards/piano in the Pernice Brothers but her now-husband Joe Pernice is the lead singer. Technically she also wasn’t the lead singer in her previous band Jale, but they didn’t really have a lead singer. Allyson McLeod of Jale later became a non-lead-singing member of The New Hardship Post, fronted by Sebastian Lippa. Come to think of it, Jennifer Pierce of Jale became a non-lead-singing member of Chappaquiddick Skyline…that just leaves Eve Hartling, but she gave up music after Jale.
Charlotte Hatherly joined the band Ash when they decided they needed a second guitarist. Apparently she was playing on stage with another band and the three lads were watching; by the end of the gig they decided she was the guitarist they’d been looking for.
That’s okay…
I see a lot of bands at Milwaukee’s Summerfest (there are probably 200-300 playing each summer).
I texted a friend that the only bassist I saw actually moving around and looking like they were enjoying themselves was Emma Anzai of Sick Puppies.
Although she does share a lot of vocals… but she deserves a mention just for the sheer energy of the performance!
Deadboy and the Elephantman had Tessie Brunet on drums. Stop I’m Already Dead on YouTube linky. Kind of a Meg White/White Stripes feel, and similarly awesome rack (sorry)
I just saw one last night - Schelia Gonzalez (that’s the correct spelling) plays sax and several other instruments for Zappa Plays Zappa.
Kylesa (she does vox too, but still)
There’s Janis Tanaka who played for a couple of mostly male bands (Fireball Ministry, Hammers of Misfortune, Stone Fox?) before playing bass for Pink. Maybe a stretch, but she’s worth a mention…she’s can play…and she’s hot.
Then there’s this…
mandolin?
Melissa Auf der Maur, most famously of Hole, has had quite the road warrior career. She toured in support of Ric Ocasic and did session work for Fountains of Wayne. Definitely a “one of the guys” rock n roll professional.
Kim Coletta played bass in Jawbox
I was just listening to them yesterday! I love Bolt Thrower.
Oh! How could I forget Tina Weymouth!?
Nope, back-up singer.
I don’t know why but all these chicks seem so ultimately cool to me. Like the highest level of cool one could be.
For what it’s worth, I play in a band with a female drummer. Also:
Filter (when D’Arcy Wretzky was playing bass for them briefly)
Eleventh Dream Day
Slowdive/Mojave 3 (though that girl did sing occasionally)
Magic Hour (Naomi from Galaxie, plus this totally awesome girl on lead guitar whose name I don’t remember)
Moonshake
Butthole Surfers (Teresa Nervosa!)
Poster Children
Black Flag (when Kira Roessler was on bass)
The American Analog Set (only the first album, sadly)
Deerhunter (I think some girl replaced Colin Mee, at least for a while)
Art Brut
Blood Oranges
The Dambuilders
The Fall (for a while, anyway)
Let’s Active always had one of Mitch’s girlfriends playing something
Jawbox
Loney, Dear (they had a girl playing mallets or something when I saw them)
Moose (for a while they had a girl drummer)
Apples In Stereo (the Hilary Sidney years)
Carsick Cars
Rusted Root
Enon (Toko’s not quite the LEAD singer…)
Shout Out Louds
Silversun Pickups
Thinking Plague
Did I miss anyone?
Time for lessons, ZipperJJ? Which insturment would you take on?
To cross into another genre of music: Willie Nelson’s piano player is his older sister Bobbie Lee, who is now 80 years old
I played bass for a summer in a garage band, where all the other members were dudes. I have big hands for a woman so I shoulda been good at it! But I didn’t care enough to put any money into it either.
I played trombone in a ska band for a short while (it was actually my project) but it was a one-time gig. That ship has sailed for sure 
Oh, thought of another one - Abi Harding, sax player for The Zutons.
Can’t believe I forgot about her!
[She’s very attractive]
She also replaced D’arcy Wretzky in the Smashing Pumpkins for some time.
Another woman in a 90’s indie band, but as an exception not on bass, but on guitar : Charlotte Hatherley from Ash.
ETA: one more female guitarist: Bilinda Butcher from My Bloody Valentine.