The best name in software, I believe, was Apple's code name BHA. The explanation for BHA appears in this post of mine from last year (starting at "One of my favorite stories...").

The second best name in software proves that Matt Groening has a lot to answer for (especially since there are still people on the internet who attribute the quote to Nietzsche): IceWeasel.

IceWeasel, noted today's boingboing.net, is a FireFox-like browser that is 100% free and uncopyrighted. Notes Wikipedia.org,

The name was coined by Nathanael Nerode as a parody of "Firefox": Fire to Ice and Fox to Weasel.