I’ve always been told to run deep cycle batteries down from time to time to extend the life so i will do that as well.
Don't do it, couchburner.
Lead/acid batteries last longest if the are kept full at a 'float' charge voltage that depends on the exact type of battery and the temperature. Any time a lead/acid battery is run down it takes some of the life out of it. The farther down it is drawn and the longer it is left that way the more the lead plates inside will sulfate and the battery loses capacity. One trick that lead/acid batteries do need once in a while is OVER charging once in a while. It's called equalize charging.
I think the run-it-down-flat advice comes from old ni-cad battery practice. But even that is pretty much obsolete, I believe.
Here's a very good read about batteries and other links on the site for good info on inverters and back-up power.
(broken link removed to http://www.windsun.com/Batteries/Battery_FAQ.htm#Battery)