Gridcoin
http://www.gridcoin.us (rewards BOINC computation) has had GPU support for a while now. Why waste electricity on hashing with your GPU when you could be contributing to real scientific research?
If you've got Nvidia you can crunch:
GPUgrid: Full-atom molecular simulations of proteins
Asteroids@home: Asteroid research - it uses photometric measurements of asteroids observed by professional big all-sky surveys as well as 'backyard' astronomers. The data is processed using the lightcurve inversion method and a 3D shape model of an asteroid together with the rotation period and the direction of the spin axis are derived.
If you've got AMD you can crunch:
Milkyway@home: Creation of a 3d map of the milkyway galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science.
POEM@HOME: Models protein folding using Anfinsen's dogma
There's also some multi-gpu compatible projects:
Collatz Conjecture: Attempting to disprove the Collatz Conjecture
Einstein@home: Search for spinning neutron (pulsars) stars using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite
PrimeGrid: Search for prime numbers. Primes play a central role in the cryptographic systems which are used for computer security. Through the study of prime numbers it can be shown whether current security schemes are sufficiently secure.
SETI@home: Search for Extraterrestrial Intelligence (SETI)