WARNING: POSSIBLE SPOILERS FROM ULTIMATE X-MEN #22. READ AT YOUR OWN RISK.
Kitty mentions that there are 20 mutants left at Reservation X. Everyone else that was present took the cure. We know 15 of them. They are currently divided, most in support of Kitty Pryde, a minority siding with Mach Two.
Reservation XKitty's Group - 13 mutants
Kitty Pryde - Shadowcat (she'll always be Shadowcat to me)
Jimmy Hudson - Diet Wolverine
Ororo Munroe - Storm
Marian Carlyle - Rogue
Seth Vale - Black Box
Hisako Ichiki - Armor
Amara Aquilla - Magma
Sam Smithers - Blackheath
Five unnamed mutants*
Mach Two's Group - 8 mutants
Nomi Blume - Mach Two
James Proudstar - Warpath
Betsy Braddock - Psylocke
Shola Inkosi - no code name?
Paige Guthrie - Husk
Bobby Drake - Iceman
Kenji Uedo - Zero (unknown if this is the same Zero from the MLF)
Scott Wright - Micromax
*Since we don't see the other five leaving with Nomi in UXM #22, it's assumed they're part of Kitty's group.
Some mutants, in addition to the thousands of SEAR residents who took the serum, are still active in Tian, under the lead of Jean Grey and Xorn. And maybe also Zorn. They are known as the Runaways by SHIELD.
TianRunaways - 3 mutants
Jean Grey/Karen Grant - Marvel Girl (she'll always be Marvel Girl to me.
Derek Morgan - Guardian
Liz Allen - Firestar
Others are part of Quicksilver's Brotherhood. Aside from Quicksilver himself, they haven not been seen since Ultimate X, but it is assumed that they are still active. At the end of Ultimatum, they were based out of Wundagore, and Pietro mentions going back to Wundagore in UXM #5.
BrotherhoodQuicksilver's Brotherhood - 4 mutants
Pietro Lehnsherr - Quicksilver
Victor Creed - Sabretooth
Teddy Allen - Blob Jr.
There are also mutants who have been seen recently, and it is unknown if they have taken the cure. However, given the fact that they are established characters, the fact that we haven't heard from them most likely means they are still out there.
Missing in ActionSeen Recently - 4 (maybe 6) mutants
Piotr Rasputin - Colossus. Last seen in UXM #10, killing a guard. Unknown if he survived the Nimrod attack on the camp.
Alex Summers - Havok. Last seen in UXM #12, in Sinister's custody.
Miranda Leevald - Stacy X - Last seen in UXM #11. Unknown if she survived the Nimrod attack.
Madrox - Last seen in UXM #7, building helmets for Quicksilver.
Nathaniel Essex - Sinister. Still unknown if he's a mutant. Last seen in UXM #12, bowing to Apocalypse.
Layla Miller - possibly not a mutant. Last seen with Sinister in UXM #12.
Seen Not So Recently - 13 mutants
Geldoff. Last seen in USM #44.
Bishop. Last seen in UXM #80, being approached by future Bishop.
Elliot Boggs - Magician. Last seen in UXM #74, leaving the X-Mansion.
Pyro. Last seen in Ultimates 3 #5, losing his hands to Valkyrie's sword.
Stryfe. Last seen in UXM #87.
Jubilee. Last seen in UXM #98.
Sasquatch. Last seen in UXM #95.
Shaman. Last seen in UXM #95.
Snowbird. Last seen in UXM #95.
Sunfire. Last seen in UXM #95.
Aurora. Last seen in UXM #95.
Lana Baumgartner - Li'l Bombshell. Last seen in USM #151 at MHS.
Lori Baumgartner - Momma Bombshell aka Mombshell. Last seen in USM #9.
There are other mutants that are not technically accounted for. For instance, Karma and Northstar are not named in Ultimatum #3 as having died, but it's assumed that they did. There are also plenty of lower tier Brotherhood members that are only seen a few times (or less) - many even without names. There were at least 20 new students at the Academy in UXM #81, it's unknown who they are, if they're alive, or if they were even mutants. We also don't know how many of the Morlocks, or which ones, Nightcrawler was able to save, or who of the MLF is still alive.
This list only covers the current cast of the book, in addition to the X-Men and major Brotherhood characters.
That makes the current total at least 28, probably somewhere closer to 35, active and named mutants.
I will update it as we learn more. Let me know if I'm missing anyone.
Updated 2/13/13 to add changes from UXM #22