Chromium is the open source version of Google Chrome. You can download more recent updates than the commercial version.
gnuplot is a good graphing program. It produces much better plots than, say, Excel. It runs anywhere. It's scriptable. You should try it.
ImageMagick is a command line utility useful for batch processing images.
Apple's music playing program. It is very basic and missing many needed features, but all the other programs are worse. If you have an iPod, you are pretty much stuck with it.
textutil is a useful OS X text conversion program. It works with txt, html, rtf, rtfd, doc, docx, wordml, odt, and webarchive files.