I just finished a MySql Automation Filter perl script with it's companion MySql Admin script.
The Admin script is a console based menu driven program that uses your current list of files in your "done" directory to create a list of file names and sizes for use by the filter script.
The filter script checks about to be downloaded files against the list of file sizes and if it finds a match it doesn't download the file.
The Admin script will also list any dups you may have in your "done" directory so you can clean up if you wish.
Using MySql opens up a lot of other possibilities. The scripts contain a lot of example code that you should be able to use to do other functions.
You could for example create a database containing files from many different directories you have so no dups are downloaded. You could also have a script run from cron on a regular basis that updates this list.
I have been running this script for a week now with no problems, I would appreciate any bug reports you can provide.
The scripts are available on the script page at the project site:

http://napshare.sourceforge.net/scripts.html

Enjoy!