Below the cut is my list. Reading almost all of these I thought 'this is one of the most wonderful books I've ever read'. Not just of SF, not just of recent SF, but of anything.
I've limited myself to no more than one per author.
Snow Crash: Neal Stephenson
Light: M John Harrison
A Fire Upon the Deep: Vernor Vinge
Cloud Atlas: David Mitchell
Red Mars: Kim Stanley Robinson
Magic for Beginners: Kelly Link
Anvil of Stars: Greg Bear
China Mountain Zhang: Maureen McHugh
Four Ways to Forgiveness: Ursula Le Guin (not essential but I had to get her into this list)
Revelation Space: Alastair Reynolds
Black Man: Richard Morgan
Player of Games: Iain M Banks
The Separation: Christopher Priest
Four Hundred Billion Stars: Paul McCauley
Permutation City: Greg Egan
Air: Geoff Ryman
Salt: Adam Roberts
Body of Glass: Marge Piercy
The Parable of the Sower: Octavia Butler
Vurt: Jeff Noon
I am sure that River of Gods belongs on here, but I haven't read it, though I know I will soon. Only a quarter of these are by women.
I also really liked Mother London, by Michael Moorcock, which was published in 1988, but I'm not sure it's essential SF.
ETA: I've added Vurt by Jeff Noon, and deleted Timescape for being out of range
