Macstories has an article on an interesting new preference Pane for OS X Lion RestoreMeNot, which is free and allows you to individually disable OS X Lion Restore Restore for Each Application of your choice.
Personally I think this should have been built into OS X as I have had some issues with Restore and certain apps (Rapidweaver will open two instances of my site, and crash if I try and save, and the Core OS X service keeps trying to open the last installer that was opened instead of the one I am trying to open) so this is a very useful little tool.