The gnome-terminal program sticks that nub there itself. It started doing that sometime during the transition to Gnome3, and when I realized it wasn't my window manager or desktop environment but the program itself, I was annoyed enough that I looked for an alternative.
~~Roxterm is currently my terminal emulator of choice.~~
[UPDATE]: I'm back to using gnome-terminal. More recent versions of gnome-terminal (or perhaps GTK?) no longer add the nub, and the Roxterm maintainer has just stopped development due to time constraints and a tricky incompatibility with recent GTK.