TextSoap is one of several applications that offers text filtering that allows you to have control over how you clean up your text. There are more than 100 cleaners built into the software, the ability to create customized cleaners, and integrates with Automator and AppleScript.
In honor of Macworld 2009, TextSoap 6 is currently on sale for 15% off the retail price of $39.95 for a single seat and $69.95 for a family pack through January 16. Use the code MACWORLD2009 when purchasing the software. TextSoap 6 requires OS X 10.5 or later.