jquery.js = Pretty and easy to read :) Read this one.
jquery.min.js = Looks like jibberish! But has a smaller file size. Put this one on your site.
Both are the same in functionality. The difference is only in whether it's formatted nicely for readability or compactly for smaller file size.
Specifically, the second one is minified, a process which involves removing unnecessary whitespace and shortening variable names. Both contribute to making the code much harder to read: the removal of whitespace removes line breaks and spaces messing up the formatting, and the shortening of variable names (including some function names) replaces the original variable names with meaningless letters.
