Version 1.1: Added preferences : timer interval and option to save checked applications upon exit. Added a donate... button; added a 'stop hiding' menu item which, when checked, suspends the timer.
HICKSDESIGN Agreed about a preference pane or menubar item. This is a great app, it just needs itself to be more hidden, rather than taking up dockspace (Version 1.1)
STEVEN JAY COHEN Instead of a menubar item, you should consider a Preference Pane. After all, most people who prefer to work this way will leave it running all the time.
I use LiteSwitch for this feature alone. Single Application Mode just makes my life easier.
Seriously though, consider a PrefPane. In the end, it makes the most sense for this sort of application. (Version 1.1)