The wmctrl program allows you to programatically bring a running application to the foreground on Linux. It works even with compiz enabled, and will switch to the virtual desktop that the application is running in before bringing it to the foreground. This makes it a perfect utility for mapping keyboard shortcuts to quickly switch between applications you leave running all the time.

To install wmctrl on Debian:

apt-get install wmctrl

For example, to switch to Thunderbird:

wmctrl -a "Mozilla Thunderbird"

The -a argument makes wmctrl switch to the first window it finds with the provided string in its title. See wmctrl's manpage for more information.

You can map a command like this to a keyboard shortcut using the (in Debian) System -> Preferences -> Keyboard Shortcuts utility.