If your web application is JavaScript intensive (these days most apps are), it will be a good idea to minify the JavaScript and CSS code. A minification tool reduces the byte footprint of the code without impacting the semantics. YUI Compressor is the best JavaScript minifier out there.

The product I work on at Yahoo! is pretty heavy on JavaScript and YUI Compressor gives me almost a 50% compression ratio, so the savings are significant.

$ du -hs foo*js
140K foo.js
216K foo_src.js

As you noticed, I keep the original source in CVS with a file name like foo_src.js. During build, YUI compressor is run on foo_src.js and foo.js is generated. The application includes the compressed version, foo.js.