After pressing F11 to enter fullscreen, the window stays small and becomes irresponsive. The issue is 100% reproducible.
I have reinstalled my system many times, trying different distributions and versions, but alas no luck. Proved to be affected: Ubuntu 12.10 and higher and it's derivates, Fedora 20.1
This bug affects any version launched from the New Launcher.
Note that fullscreen works with OpenJDK 64bit in Ubuntu 12.04 and it's derivates, and also in CrunchBang 11.
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CubeTheThird
Not exactly the same, but essentially a duplicate of MC-2067. This issue is caused by either Xorg, your desktop manager, your graphics drivers, or the LWJGL libraries that Minecraft uses (or a combination of these). I can somewhat confirm that fullscreen doesn't work (I have sometimes achieved it), but unfortunately it is not an issue that Mojang can deal with, as it does not pertain directly with Minecraft.
migrated
I have now confirmed that this issue is valid for all but KWin and OpenBox (and possibly some less used lightweird ones). Should not be marked as duplicate, because it does not duplicate anything, and the "duplicated" issue is different. This is a bug in the way Minecraft makes it's wondows, and will affect all Ubuntu users.
CubeTheThird
I have changed the link from duplicate to "relates to". Please note that this does not affect all Ubuntu users, as I use Ubuntu and have been able to successfully play with fullscreen.