.js/.css = Pretty and easy to read. .min.js/min.css = Looks like jibberish! But has a smaller file size. (Use this one)
The second one is minified, a process which involves removing unnecessary white-space and shortening variable names. All this is done in such a way that it doesn't affect the way the code behaves when run, in any way.
Just to point out as well, you are better using the minified version (.min) for your live environment as Google are now checking on page loading times. Having all your JS file minified means they will load faster and will score you more brownie points.