Using 'Tab' when you have multiple unit types selected will cycle between them. 'Shift'+'Tab' will cycle backwards.
Hitting 'F1' selects an idle worker. 'Ctrl'+'F1' selects all idle workers.
You can keep HP bars turned on all the time from the gameplay options menu.
Turning on building grids in the options menu makes walling a lot easier.
'Shift' queuing commands now work with stuff like siege and burrow.
It's also possible to 'Shift' queue waypoints now.
If you have multiple workers selected, you can issue multiple build commands and they'll each build one; extra workers will continue whatever they were doing.
Hitting 'Backspace' jumps between your town halls.
'Ctrl'+'F' changes team colors to you = green, allies = yellow, and opponents = red.
'Ctrl'+'Alt'+'F' brings up a framerate counter
Terran
Calling down mules directly on minerals will allow them to auto-mine.
SCVs can be set to auto-repair by hitting 'Alt'+'R'.
Zerg
Have your queens hotkeyed with your hatcheries so you can inject larvae without looking at your base.
You can give eggs their own move command so that the units will move there once they hatch, regardless of what the hatchery's rally point is.
Protoss
Have one hotkey that just contains all your buildings, then you can chrono boost with by clicking on the building's wire frames without looking at your base.
Pressing 'W' selects all your warpgates (and excludes normal gateways).
You can tell units warping in to move before they're done warping in, and they'll move there as soon as they finish.