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There are a couple of applications that I find myself marking as "Always on Top" every time I use them, so I wonder if there is a way to automatically set them as so, whatever way I start them (menu, shell, gnome-do)?

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up vote 10 down vote accepted

If you're using Compiz, you can go into CompizConfig Setting Manager, and enable the Windows Rules plugin, and then add something like class=Gnome-terminal under "Above" to make all Gnome Terminal windows Stick on Top. (You can click the + button and use the grab feature to figure out the class name for various applications if it's not obvious.)

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Hmpf, bah, the name of this plugin is translated totally wrong in Dutch... :-( – JanC Oct 15 '10 at 3:09
Very nice! I found that "sticky" is actually "always on this workspace" if anyone is wondering. Also worth mentioning is that if you are using the title of a window, i.e. title=This Window Title, you do not quote it. Use it just like I wrote it. – Elijah Lynn Mar 12 '13 at 16:02

There is a more general solution, working with a EWMH/NetWM compatible X Window Manager (all commonly used wm are included).

The solution concerns the use of the wmctrl application (found in wmctrl package).

You can set the "on-top" property with

wmctrl -r "window title" -b add,above

There is, however, some work left to automate the process.

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seems like a good alternative, when compiz is not used. nice! – Decio Lira Oct 15 '10 at 13:15
This is the best option for me because I can create a bash script or a keyboard shortcut (which I did) using this command and that way I can use it when I need it but not when I don't. I did make a change though...I wanted a shortcut to turn always on top for the active window and only when I needed so here is my command. wmctrl -r :ACTIVE: -b toggle,above – Michael Tunnell Aug 23 '13 at 21:26
arguments "add,above" is not working for me. but arguments "toggle, above" works (toggles). – Palani Jan 7 '14 at 8:42

You can use something like Devil's Pie (Ubuntu package).

See frabjous answer about how to do it with Compiz.

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