Since the keyboard shortcuts are not yet configurable, and will remain so for some time, here's a list of them. They should get somewhat optimized, though.
File -> Open (Control + O)
File -> Save (Control + S)
File -> Save As (Control + Shift + S)
Program -> Compile (Control + W)
Program -> Run (Control + R)
Program -> Compile and Run (Control + E)
Program -> Clean (Control + D)
Program -> Show java output
Settings -> Patch sprites (F5)
Settings -> Check configuration
Settings -> Basic configuration (F7)
Settings -> Editor configuration
Help -> About (F1)
Help -> About Qt (F2)
Help -> Check for updates (F3)
Suggestions, as always, are welcome.