Mac OS X Lion: Restore is undoubtedly one of Lion's best features, but if you find certain apps restore themselves when you'd rather not see them immediately on boot, RestoreMeNot lets you specify apps that you want to keep from launching at boot.
RestoreMeNot couldn't be simpler. Just install it, then head to its preference pane to select apps. Just hit the plus sign to add them to the list, and the next time you start up, they'll be completely closed -- without you having to disable restore altogether.
RestoreMeNot is a free download for Mac OS X Lion only.