I think I've partially solved this by updating the
/usr/share/applications/nautilus.desktop file, and changing this line:

MimeType=inode/directory;application/x-gnome-saved-search;
to be:
MimeType=inode/directory;application/x-gnome-saved-search;x-scheme-handler/smb;x-scheme-handler/ssh;

Then running sudo update-desktop-database to update the file
/usr/share/applications/mimeinfo.cache

Hat tip to the instructions here: http://jarrpa.net/2011/10/28/creating-
custom-url-handlers-in-ubuntu-11-04-11-10-gnome-3-0/

I'm not certain that this entirely works (it's not quite deterministic),
but I'll give the machine a rebot and see if its stuck.

This works because this patch was added:
http://bazaar.launchpad.net/~unity-team/unity-lens-applications/trunk/revision/202

This calls AppInfo.launch_default_for_uri (orig, null), which looks up
the native gnome url handler.

Something that really isn't documented anywhere - to get debug output,
find the program like so:

david@silver:~/unity-lens-applications-0.4.12$ ps axfu|grep lens
david    15396  0.0  0.6 206424 13268 ?        Sl   01:04   0:03 
/usr/lib/unity-lens-applications/unity-applications-daemon

Kill it and  restart it, and then it will produce output like this:

david@silver:~/unity-lens-applications-0.4.12$ kill 15396
david@silver:~/unity-lens-applications-0.4.12$ 
/usr/lib/unity-lens-applications/unity-applications-daemon 
(process:4185): unity-applications-daemon-DEBUG: daemon.vala:256: Building 
initial application menu

Leaving the program running, run the command that isn't working, and
this will get outputted:

(process:4185): unity-applications-daemon-WARNING **: daemon.vala:744:
Failed to launch URI ssh://throium

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Bugs, which is subscribed to Ubuntu.
https://bugs.launchpad.net/bugs/770126

Title:
  Alt+F2 - ssh:// and smb:// access doesn't work in Unity (should open
  Nautilus)

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