What you're usually interested in is the size after compressing with GZIP (you should configure your web server to perform the compression).
EDIT: since the original time this question was asked, 2 new minifiers have been released. They're both usually at least as good as, if not better than, the YUI Compressor.
- Google's Closure Compiler. Includes an aggressive advanced optimization mode that's sometimes applicable.
- Microsoft's Ajax Minifier (search this page for "minifier")
- UglifyJS, chosen by the jQuery team for the official 1.5 release
Yahoo's compressor, for a combination of safety, and decent compression.
Packer does have an encoding feature that generates an even smaller file. However, it's only effective if your web server does not support gzip or deflate compression. With gzip / deflate, YUI and Packer generate files that are about the same size.
Look at this question for a good answer: