There are many tools to help you minify : JSMin, Rhino, …. , YUI Compressor
After some reasearch and inclination towards Yahoo, I decided to use YUI Compressor. Its a simple Java command line tool with good documentation (Link).
Here is how to run the batch file:
1. Download the latest YUI Compressor Jar file
Note: Edit the batch file to make sure its pointing to the right (exact name) jar file
3. Run the batch file (double click) and you will see a new directory called packed with all the minified files. You can then choose to either manually replace the files with newly minified files or make changes to your application to use minified files.