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