What distribution are you running? Do you want to remove data (pictures/documents/music, etc) or Linux applications? You can't just delete a directory in Linux or you're asking for trouble.
If you can clear out data, it should be in your /home directory. If you want to remove applications I'd use whatever package manager your distribution uses; yast for SUSE, Synaptics for Debian based Distros, eg, Ubuntu. This would allow you to remove the software cleanly. You can also tidy up by removing browser histoey files and cookies (not a lot of space freed off really)