I love GeekTool, but ran into a roadblock when one of my geeklets caused it to freeze on startup, and I couldn't remove the offending widget from within the System Preferences panel. So, after digging around, I discovered that the geeklets are stored as plist files at ~/Library » Preferences » org.tynsoe.geeklet.*.
You can open these files in the Property List Editor (or PListEdit Pro), and look through the entries to find the problematic script, and delete the entry (or fix it, I assume). Then, save the file, restart GeekTool from System Preferences, and you should be good to go.
After having to do that a few times, you will probably figure out what is causing the freeze and be able to fix your script. For me, using $>tail -f <file_name>, caused it to freeze, but using a file geeklet with the same filename, I was able to get the same result.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20091008203804291