xclip is a command line interface to the X11 selections (X11 clipboard). It can also be used for copying files, as an alternative to sftp/scp, thus avoiding password prompts when X11 forwarding has already been setup. xclip reads from Standard Input or from one or more files and copy it to the X11 clipboard making it available to the X applications.
BasKet Note Pads is a free opensource notepad/scrible pad software for Linux. BasKet can be used as a manual clipboard. This means that you can drop files of all kinds inside. They can be grouped in different tabs. BasKet is very simple to use and easy to differentiate between notes by setting tags, priorities and flags.