On Arch, the system-wide shortcuts are stored in /usr/share/applications. Each one is a .desktop file with a few parameters. user-specific icons are stored in ~/.local/share/applications. I downloaded eclipse and extracted it in my home directory, so I'll use eclipse as the example application.
Create the .desktop file
Paste this in:
[Desktop Entry] Encoding=UTF-8 Version=1.0 Type=Application NoDisplay=false Exec=/path/to/eclipse/eclipse Name=Eclipse Comment=Launcher for Eclipse
Each line is pretty self-explanatory. Edit to suit your needs. As soon as you save the file, you will be able to see your new shortcut in the list.
(Optional) Give the shortcut a nice-looking icon: You probably noticed that your icon is an ugly diamond. To pretty it up, you simply have to add one more line to the desktop file.
Your application may have included a png icon, but to make it really look nice, you should grab an SVG file of the logo from somewhere. Arch has a very simple packaging process which lets you examine all of the package building elements through their webpage at http://www.archlinux.org/packages/. I was able to grab the SVG which the package uses like this:
wget -O eclipse.svg http://projects.archlinux.org/svntogit/packages.git/plain/trunk/eclipse.svg\?h\=packages/eclipse