Ubuntu's Gnome desktop uses GVFS to mount those shares.
You should be able to use the following command to mount your shares. If you have a persistent home directory, you can add this or similar to some startup files.
The mount should be available under your home directory, in
/home/username/.gvfs. For example, on my system I did the following:
$ gvfs-mount smb://my-home-server/my-share
$ ls -F ~/.gvfs
my-share on my-home-server/
So that share is directly accessible (on commandline and in the desktop environment) via the mountpoint
/home/username/.gvfs/my-share on my-home-server.
According to several sources, if you are using this over SSH or another situation where you aren't running the full Gnome setup, you may need to use dbus-launch to mount the share:
dbus-launch gvfs-mount smb://server-name/share-name