How to add custom links in the left pane of Nautilus?

Select the folder you want to link, then go to the top menu bar and select Bookmarks -> Add Bookmark.

When inside the folder that you want to bookmark, go to the top menu bar and select Bookmarks -> Bookmark this location -- or Ctrl+D.

You have to go into the folder you want to add, and then press Ctrl + D, contrary to every other file manager on earth.

Please, apply the principle of least astonishment here and go back to something sane. You can remove these by commenting out the corresponding lines in ~/.config/user-dirs.dirs.

Source: blog post Ubuntu 12.04: Adding Bookmarks/shortcuts to left sidebar of Nautilus manager (2012-05-05)

You may just drag'n'drop any folder you want to appear in Places bar. This works for remote folders too. Or make a bookmark entry with Ctrl+D shortcut.