Postpone Break: These two menu commands defer the next due break by a few minutes. The number of minutes comes from the Break Appearance preferences, and the items are disabled if the corresponding checkbox is unchecked.
Skip Break: Similarly, this command skips to the next occurrence of the upcoming break, if that option is checked.
Reset All Breaks: This command changes the next due time for all breaks to be their frequency from now. So for example if you have a break that occurs every hour, it'll become due an hour from now.
Stop Sound: If a sound action is currently playing, this will immediately silence it. Useful if you have a song or other long sound set for a break, and don't have a fade-out action set.
Check for Updates...: This command manually checks to see if there are any updates to the app available. Note: this item isn't included in the Mac App Store edition.
Setup Assistant...: If you ever want to restore the default breaks or get a reminder on how to enable the keyboard idle detection, this command will re-display the Setup Assistant window.
Quit Time Out: This will quit the app, so you won't get any more breaks until you open it again. (Might be better to pause instead?)