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The latest VLC 2.0 got support for MPRIS v2, meaning it can make use of the Ubuntu Sound Menu or other docks / extensions that support it (like the GNOME Shell Mediaplayer extension):

VLC 2.0 ubuntu sound menu

vlc 2.0 gnome shell mediaplayer extension

But the MPRIS v2 Dbus interface is not enabled by default in VLC 2.0, so here's how to enable it: in VLC go to Tools > Preferences, select "All" under "Show settings" (bottom left), then navigate to Interface > Control Interface and check the box next to "D-Bus control interface":

vlc preferences

Then click "Save", restart VLC and it should now show up in the Ubuntu Sound Menu or GNOME Shell Mediaplayer extension, etc.

VLC uses a tray icon by default which is kind of useless now - if you want to disable it, go to Tools > Preferences > Interface and uncheck the "Show systray icon" box:

vlc preferences

VLC 2.0 is available in the Ubuntu 12.04 Precise Pangolin repositories and in a PPA for Ubuntu 11.10 Oneiric Ocelot users.