You could use the
mount command in a start up script and put that in the Startup Application Preferences.
mount is perfectly capable of mounting remote file systems (if you provided it with the right options and all necessary packages installed).
An alternative to mount in your startup script is gvfs-mount . You can mount nautilus-type URIs with that - just like nautilus does. It is installed by default on most Ubuntu systems.
-u option unmounts the argument,
-l lists all mounted file systems,
--help gives you more options.
Finally the file
/etc/fsatab is usually used to mount file systems statically. If your remote server is reliable you might want to take a look at fstab. It will slow down your boot time drastically if the server is slow or offline but it has the advantage of making the file system available quiet soon (before gnome or X are even loaded, e.g. for use in scripts).
Check out Gigolo . It has the capability of auto-mounting a bookmark, whenever the bookmarked filesystem is present.
sudo apt-get install gigolo # or use the install link above
gigolo. There is an option in the preferences that puts it into autostart and another to activate the tray icon. Check both. Then add your bookmark.
Here is a screenshot: