I don't enjoy saying this, but customizing Nautilus is not high on the list of priorities of GNOME devs at the moment. If you're unwilling to modify the source code of Nautilus, I very strongly recommend that you consider installing Nemo. Nemo is everything that Nautilus was, and more.
Installing Nemo is easy: search in the Software Centre (where it's called files) or -
sudo apt-get install nemo
In Nemo, there's only a single combined list for Places and Bookmarks:
Therefore, adding an entry to the Places menu is exactly the same as adding an entry to the Bookmarks. Adobe's answer covers the configuration file, but any other method (CtrlD, dragging-and-dropping, etc.) works just as well.
For example, here's my file:
$ cat .config/gtk-3.0/bookmarks
There's a distinction in the dialog box shown for opening files in most applications:
I think the entries for the home folder, Desktop folder and filesystems are hardcoded. They can't be removed, at any rate (the option is disabled for them, but enabled for the others).
Nemo uses the same icon for a folder in both the sidebar and the main view. It's called an emblem (the icon next to the name):
You can set any image here:
In this case, the icon for the Templates folder is a 1.4MB wallpaper.