You know what I've got used to do to know when the program had completed some operations? To put the mouse pointer over a different menu option than the one selected. As soon as it highlights I know the program is back to his externally-conscious state. Ouch..
+1 Great minds think alike?
Another problem that I find particularly annoying is the progress bar sticking at 99% finished for a longer time than than the first 98%. If the final 1% takes longer to complete than the first 99% then obviously the 99% was only 50% or less. Every time that I experience this I begin to wonder if the program has gone into an endless loop and I feel compelled to kill it and start over. The only thing stopping me is the knowing from experience that I will end up in the same place.