OK. So you seem to be talking about a graphical file manager "nautilus" in your case. I was already wondering what exactly you were trying to point at with your mouse.
Using nautilus there are most probably two different tasks you might want to achieve and I'm not sure for which one you are aiming. Those possibilities are:
associate a program with a given file type. Allowing you to open the file with the specified application. Either by selecting it from the "open with" entry of the context menu that opens after a right-click or by double-clicking on the file.
add a new entry to the context menu. Like open Terminal here when right clicking on a folder or the like.
While the whole framework working in the background is a rather involved collection of specifications involving
.xml files containing metadata about known mime-types, installed applications and the mime-types they are able to handle practically most probably you won't have to manually touch any of these as other tools at your disposal will most probably add the appropriate entries for you.
As some background knowledge sure won't hurt most probably studying the specs referenced below should help you getting started:
Essentially it boils down to the fact that there are two databases involved to which newly installed applications can add new information.
One listing any known mime-types and a description of how to discover if a given file belongs to this mime-type.
And another one listing any installed applications along with the mime types they can handle. It's this database from which the entries in the "Open with" entry of the right-click context menu are generated on the fly.
Additionally for every known mime-type one of all installed applications known to be able to handle it is designated as the default application to handle this type.
This is not only the one that will open on a double click, but also the one that will be shown as the top entry of the right-click context-menu.
Adding any other other application to this list using nautilus shouldn't be to complicated - just use the context-menu entry "open wit other application..." and either choose from the list of known applications or add your own.
Note that there is also an option to remember the selected application as the default application for the given mime-type.
using the command-line
There is also a command-line tool
xdg-mime (be sure to have xdg-utils or whatever the package is called in your distribution installed to use it) that allows to manipulate the database entries.
Best take a look into the manual pages or over here on stackoverflow (see: How to use the xdg-mime command)
The good news about the modifications made with either tool is, that your settings will also work if you switch from gnome to kde or any other desktop environment that adheres to the spec.
Even more information about the ongoing process of unifying system and user settings information management between different desktop environments can be found on: http://www.freedesktop.org
You want to add a new contex-menu entry allowing you to perform some arbitrary operation either just with a single selected file or folder or even with a whole selection of files like zipping them into an archive or whatever.
Unfortunately AFAIK there is no unified way shared between all desktop environments to perform such a task.
Using nautilus you'll most probably want to use the nautlius-actions extension that should be available (although maybe with a slightly different name) in the repositories of your distribution.
Using this extension you will be provided with a point and click interface allowing you to perform arbitrary operations on a selection of files or folders selected by arbitrarily chosen conditions.
That fact that I don't know any other option doesn't necessarily mean there is no other possibility for case 2. Things still seem to be developing pretty fast in this sector and I haven't kept up with newest trends for a long while.