I've always had trouble keeping my workspace clean, especially if I'm the only one using it.
Currently I have divided my workspace up into three parts . . . electronics bench, mechanical work bench, and random junk bench.
I find having drawers, and labels printed on those drawers, encourages me to put stuff in a proper place and keep it there.
A side story . . . at the CMU robotics club we always had like 20-40 people always using the workspace and making messes . . . it was so bad that most people didn't even know there were 'keep workspaces clean' labels taped to the table tops cause of the clutter . . .
Then one day someone got the genious idea of taping big pics of bikini clad women to the tables . . . suddenly the tables were much cleaner
but someone took offense to it and tore them up