1. Do I have some way to influence which inputs are chosen? For example, can I choose 10 "virgin" coins for a 500 BTC transaction, instead of thousands of 0.01xxx inputs?
2. Can I somehow view the details of my wallet? I imagine that I could send the offending small inputs away to a different wallet, if I only knew their exact face value and the order in which they appear in the wallet.
3. Is there any other way to "clean" my wallet, or reorder the items in it so that the offending items will be selected last instead of first?
Some of the alternate clients provide 1 and 2.
3. unfortunately not exactly, the standard client has it's own way of selecting inputs. I think there's a patch around that completely ignores small amounts, maybe there are more patches that do other things.