Perhaps you need to white list it again. Unity and GS both keep you
from running apps from the system tray/ notification area by default.
Perhaps you need to re-enable this.

See: www.webupd8.org/.../...able-notification-area.html

I am not sure if this will re-enable the Bookmarks themselves because I am
not sure what the bookmarks are on your system.

My bad - I should have been clearer.

This wasn't in the systray/notifications area. In 11.10, on the left end of the
Unity application bar, I had the following: File, Edit, View, Go, Bookmarks,
Help.

Bookmarks was the drop-down menu of my user-defined nautilus folder bookmarks.
It's still there if I'm actively using nautilus, but in 11.10, nautilus wasn't
even open - those bookmarks were just always available on the desktop
applications bar - very handy and convenient. I don't remember tweaking
anything to get it there, but that's also a possibility.

In 12.04, it's gone. Ideas?

Just discovered an acceptable answer. Right-clicking on the Home/File
Manager/whatever icon in the launcher presents a quicklist of the nautilus
bookmarks. Pretty cool.

Yes. They've tweaked a few things. I personally remove the global menu, so
all menus are in the application window instead of the panel. I find it
confusing and time consuming to click to shift focus when you have two
windows open. I am not a fan of Nautilus. It has been dumbed down to the
point of being useless. It is difficult to change settings and has so
little useful information by default. I use Dolphin which is more full
featured and easy to configure. I love the filter bar at the bottom. Type
jpg in it and I see only jpg files. Very handy for moving things around.