There are several very popular tools for compressing/minifying your JavaScript and CSS.
- Yahoo YUI Compressor
- Microsoft AJAX Minifier
- Google Closure Compiler (JavaScript-only)
All are very powerful -- you can find comparisons of them quite easily. All are command line tools, so they can be easily integrated into your run automatically when you build or publish your website.
You can also find many websites that run these tool for you, which will save you the time of having to install/configure. This also helps if you aren't familiar with using command line tools.
Personally, I've always had YUI Compressor configured to run when I build and recommend itused YUI Compressor.