Most commands will have a length of time that you can set. For instance, the Repair command allows you to set how many time units you spend repairing a certain system. Other commands affect time differently, depending on the command. Most commands that don't have a time option take 10 time units to complete. Any that have a different duration will mention this in the command description.
One exception is the Warp command. The number of time units taken depends on two factors; the distance traveled and the speed traveled at. Warp commands calculate time usage with the following equation:
For example, if I was to travel a distance of 10 squares at warp 5, the time spent would be 2 units. Thus it is possible to travel roughly 990 squares at warp 9.9 (the highest warp speed possible). I wouldn't advise doing this however, as you could travel through several different sections of space not knowing what you will run into. Note that the Goto command also uses this equation.