This will be changed significantly in 12.04. As additional answer to question 2
Three out of the bottom 4 icons can be adjusted as noted by changing the default - internet browser;email;music, the photo viewer choice is coded in the source
If your preferred is not listed in System Settings ... you could probably track down in gconf-editor but no need. Each of the 3 is set from 1 specific mimetype, so it can be altered in
~/.local/share/applications/mimeapps.list in the
[Default Applications] section.
Generally speaking most apps for these types would register when installed though a quirk in gnome3 is that if the app's .desktop doesn't have an Exec= line that ends with
%<letter>it won't show as a default choice so that's something else to check