An addon for Firefox that scans your bookmarks for duplicates, empty folders, and dead links. Gives you the option to merge or delete them. Pointedly advises you to back them up first.
An open source GUI app for Linux which helps you clean out old tempfiles and logs that are taking up disk space. The fact that this also makes for good personal information hygine is parenthetical. Can clean out files for Firefox, bash, Beagle, Flash, and more.
Paste in HTML, CSS, or JavaScript, hit "Clean", and it'll clean up whatever you gave it so that it's more readable.