Use alltray: [quote] Dock any application in the tray
With AllTray you can dock any application without a native tray icon into the system tray. It works well with GNOME, KDE, XFCE 4, Fluxbox, and WindowMaker. [/quote]
PS.
I prefer to use switch-or-exec plugin in Sawfish at hot-key: I will press hotkey, Sawfish will switch to application desktop area and then bring application window. If application is not running, then Sawfish will run it. Configuration is very simple: regexp for window title or window properties to find application window and command line to execute when application window is not found.
For example, I can press "Alt-Shift-e" to switch to editor window to enter few notes. If editor is not found, then new editor will be run. When I will finish, I will press "Alt-Shift-b" to switch back to browser, "A-S-m" for mail, "A-S-i" for IDE, "A-S-t" for terminal, and so on.