libcanberra-gtk2-0.10-3.fc10.x86_64 I believe it's libcanberra doing this on its own. When a tooltip disappears, I get the same sound as when closing a window. This shouldn't be the case though.
That was actually a bug in metacity which draws its own tooltips and didn't set the type hint properly. I have prepped a patch for that: http://bugzilla.gnome.org/show_bug.cgi?id=593358 It's commited to rawhide's metacity but not built yet because of some e-d-s/openssl breakage