If you aren't already aware of them, you might like to know about Clecos: http://www.rivetsonline.com/cleco.html which are to sheet-metal working what pins are to dress-making. They're a temporary fastener to hold 2 pieces aligned together while they are drilled or riveted.
If you want a lot of holes evenly spaced, an adjustable rivet spacer is a alternative http://www.aircraftspruce.com/catalog/topages/rivspacer.php?clickkey=6495 to a sheet of perf-board, but whether the extra expense is justified would depend on how important regularity and particular spacing is.
@ca94002...thanks for that.....I could easily have expanded this to two articles with all the other tools that commenters have given. I have a leather punch and a hand reamer as you describe, so I should not have forgotten about them. But then again, if I had covered everything I probably would not have got all these comments!