I choose the option to have my reapeaks sent to a specific destination folder, then use ccleaner to delete that folders contents when it is run. (you can set it to run when you're boot up, but I prefer to manually execute it) plus its a brilliant tool to have for your comps general maintenance
http://www.piriform.com/ccleaner
I also use Mediasweeper for cleaning out my projects. Start to use this only when you are positive you know how it works.
http://www.mediasweeper.com.au/
Being anal with your project folders in the first place helps with keeping the mess down, mostly.