If you have a separate .js file, you may simply compress it with tools such as Yahoo YUI Compressor.
But, how can I compress embedded Javascript in every pages in my project?
(Copying the Javascript to a separate file, then compress, and then copy back to my page cannot be a professional solution for obvious reasons for a medium or big project)
You would normally have a build process which turns the source into a deployable form. This would include any compilation, unit tests, compression etc.
YUI compressor has a build tool for just that http://yuilibrary.com/download/builder/
Also check out ANT http://ant.apache.org/