The keys I use:
EDIT: the single most important key, originally forgotten because it's so ubiquitous: SHIFT - used to queue up orders. By holding shift literally any series of commands can be stacked on top of each other. Shift also acts as a modifier on factories so that clicking a unit's build icon will add 5 to the build queue.
Ctrl-Z: Select all units of selected type. So if you've got one fighter plane selected, Ctrl-Z will select all your fighter planes. I often use this in combination with:
Ctrl+(#1-9): Like other RTSes, you can assign Ctrl groups to units. In Supcom FA this is mostly redundant because you can draw a box around the entire map if you want. However this is useful for a few specific reasons: grouping all fighter planes; grouping all bombers; grouping all TML so that all can be launched together easily; grouping some engineers that are assigned to upgrade mexes so that you can switch their priority easily.
T: Track unit: this is a hangover from Total Annihilation, but it can be really useful. The only time I use it in a game is when I've clicked the Engineers Idle button and I can't immediately see where that engineer is. Press T and then the mousewheel will zoom in directly to his position. This is also good if you're watching a replay and you want some bomber porn.
Alt+rightclick: Attack-move: If used on an engineer, this will make him reclaim everything from where he is now to the point you click. This is exceptionally useful, and it's better than patrol because once he's finished he pops up on the Engineers Idle button. I also use this if I have shields or AA in with my ground force, to make sure that all the units move (roughly) together.
Space: Battle porn.
I'm sure there are plenty of other useful shortcuts, please post them here.
