I don't think I've ever seen this used for anything besides virus propagation, but there's a "feature" in IE that lets you encode your java script or vbscript so that someone casually browsing through your page source can't see what your scripts do. A while back I got an an amusing little malicious email that that tried to ues this trick to hide its real purpose, so I tracked down a few script decoders to see what it was really supposed to do (if I had been using Outlook + IE).

Anyway, to make a long story short
http://www.virtualconspiracy.com/
has a script decoder. But more importantly, he also wrote a detailed paper on how he reversed the encoding scheme without reversing the decoder built into IE. It's an interesting read on beginner crypto reversing that illustrates the thought process well, and also gives a good example of why "security through obscurity" is largely a stupid idea.

He also has a little Perl script that fetches and rips the latest dilbert cartoon as a GIF file from the official web page