I am using the online stopwatch found at:

http://www.online-stopwatch.com/full-screen-stopwatch/

How can I save this flash file and run it offline.

(Edited after finding the solution)

When viewing the stopwatch online, click on "Web" at top left, click "Save as", choose folder location, then click "ok".

When you double click on the saved file, your web browser will open and run the flash file.

Note: It actually created a new folder in which it was placed.