In SC2 1.2.0 they added support for customizable hotkeys. I've mapped all QWERTY hotkeys to Colemak so now it's actually possible to play the game without punching yourself in the face to build a Probe.
Save as Colemak.SC2Hotkeys in Accounts/[id]/Hotkeys. On OS X it's located in ~/Library/Application Support/Blizzard/StarCraft II, no idea about Windows.
Almost everything is remapped, only the spectator keys are unchanged I think.
Updated 2011-07-30!
[Settings]
[Hotkeys]
Sound=Control+R
LeaderNone=K
LeaderResources=P
LeaderIncome=U
LeaderSpending=R
LeaderUnits=L
LeaderUnitsLost=I
LeaderProduction=S
ObserveAllPlayers=F
NamePanel=Control+K
StatPanelResources=Control+U
StatPanelUnitsLost=Control+P
CameraCenter=Control+T
CameraFollow=Control+Shift+T
MinimapColors=Option+T
MinimapPing=Option+D
MinimapTerrain=Option+G
ReplayPlayPause=MediaPlay,MediaPause,MediaPlayPause
ReplayRestart=G
ReplaySkipNext=MediaNextTrack
ReplayHide=Control+G
[Commands]
ArchonHallucination/Sentry=K
AssaultMode=S
AutoTurret/Raven=G
Baneling/Zergling=B
Banshee/Starport=F
Bunker/SCV=L
BunkerLoad=I
BunkerUnloadAll=S
BurrowDown=P
BurrowUp=P
CalldownMULE/OrbitalCommand=F
CloakOff=S
CommandCenterLoad=Y
CommandCenterUnloadAll=S
Contaminate/Overseer=F
CyberneticsCore/Probe=J
DarkShrine/Probe=S
DarkTemplar=S
Drone/Larva=S
EMP/Ghost=F
EngineeringBay/SCV=F
EvolveGlialRegeneration/RoachWarren=D
EvolveInfestorEnergyUpgrade/InfestationPit=D
EvolveTunnelingClaws/RoachWarren=G
EvolveVentralSacks=F
Extractor/Drone=F
Factory/SCV=T
Feedback/HighTemplar=T
FighterMode=F
FleetBeacon/Probe=T
ForceField/Sentry=T
Forge/Probe=T
FungalGrowth/Infestor=T
Gateway/Probe=D
GatherProt=D
GenerateCreep/Overlord=D
GhostAcademy/SCV=D
GhostHoldFire/Ghost=T
GravitonBeam/Phoenix=D
GreaterSpire/Spire=D
GuardianShield/Sentry=D
Halt=G
Hellion/Factory=F
HighTemplar=G
HighTemplarHallucination/Sentry=G
HunterSeekerMissile/Raven=P
Immortal/RoboticsFacility=U
ImmortalHallucination/Sentry=U
InfestationPit/Drone=U
InfestedTerrans/Infestor=G
InfestedTerrans/InfestorBurrowed=G
Infestor/Larva=T
Interceptor/Carrier=U
Lair/Hatchery=I
Land=I
Larva=R
Lift=I
Lower/SupplyDepot=P
Marauder/Barracks=S
MassRecall/Mothership=P
Medivac/Starport=S
MissileTurret/SCV=G
MovePatrol=SemiColon
Mutalisk/Larva=G
NeuralParasite/Infestor=F
Nexus/Probe=K
NukeArm/GhostAcademy=K
NukeCalldown/Ghost=K
NydusNetwork/Drone=K
PhasingMode/WarpPrism=F
PointDefenseDrone/Raven=S
Probe/Nexus=F
ProbeHallucination/Sentry=F
ProtossAirWeaponsLevel1/CyberneticsCore=F
ProtossGroundWeaponsLevel1/Forge=D
ProtossShieldsLevel1/Forge=R
PsiStorm/HighTemplar=G
Pylon/Probe=F
Raise/SupplyDepotLowered=P
Rally=J
RallyEgg=D
Raven/Starport=P
Reaper/Barracks=P
ReaperSpeed/BarracksTechLab=K
Refinery/SCV=P
Repair=P
ResearchBattlecruiserSpecializations/FusionCore=P
ResearchDurableMaterials/StarportTechLab=S
ResearchExtendedThermalLance/RoboticsBay=F
ResearchGraviticDrive/RoboticsBay=D
ResearchHighCapacityBarrels/FactoryTechLab=U
ResearchHighTemplarEnergyUpgrade/TemplarArchive=E
ResearchInterceptorLaunchSpeedUpgrade/FleetBeacon=D
ResearchNeosteelFrame/EngineeringBay=K
ResearchNeuralParasite/InfestationPit=F
ResearchPsiStorm/TemplarArchive=G
ResearchPunisherGrenades/BarracksTechLab=D
ResearchRavenEnergyUpgrade/StarportTechLab=G
ResearchSeekerMissile/StarportTechLab=P
ResearchSiegeTech/FactoryTechLab=R
ResearchWarpGate/CyberneticsCore=D
Roach/Larva=P
RoachWarren/Drone=P
RoboticsFacility/Probe=P
SCV=R
SensorTower/SCV=K
Sentry=F
SetBunkerRallyPoint/Bunker=J
SiegeMode=F
SiegeTank/Factory=R
Snipe/Ghost=P
SpawningPool/Drone=R
SpineCrawlerRoot/SpineCrawlerUprooted=P
SpineCrawlerUproot/SpineCrawler=P
Spire/Drone=R
SporeCrawlerRoot/SporeCrawlerUprooted=P
SporeCrawlerUproot/SporeCrawler=P
Stalker=R
StalkerHallucination/Sentry=R
Stargate/Probe=R
Starport/SCV=R
Stim=G
Stimpack/BarracksTechLab=G
Stop=R
SummonNydusWorm/NydusNetwork=K
SupplyDepot/SCV=R
TemplarArchive/Probe=G
TerranInfantryWeaponsLevel1/EngineeringBay=F
TerranShipPlatingLevel1/Armory=SemiColon
TerranShipWeaponsLevel1/Armory=R
TerranVehicleWeaponsLevel1/Armory=F
Thor/Factory=G
Transfusion/Queen=G
TransportMode/WarpPrism=G
Ultralisk/Larva=L
UltraliskCavern/Drone=L
Unsiege=S
UpgradeToPlanetaryFortress/CommandCenter=SemiColon
UpgradeToWarpGate/Gateway=D
WarpPrismHallucination/Sentry=P
WeaponsFree/Ghost=D
YamatoGun=J
hydraliskspeed/HydraliskDen=D
overlordspeed=SemiColon