How I finally got Conkeror to be the default browser on Ubuntu 11.10.
The beginning was this bug comment: https://bugs.launchpad.net/ubuntu/natty/+source/gnome-control-center/+bug/708382/comments/4
There was also a .desktop file entry, from an answer here http://askubuntu.com/questions/45885/how-do-i-set-a-custom-browser-as-default-in-preferred-applications by 'rakete'
So it ended up being, create this file in ~/.local/share/applications/firefox.desktop
#!/usr/bin/env xdg-open
[Desktop Entry]
Version=1.0
Type=Application
Terminal=false
Icon=conkeror.png
Name=Conkeror
Comment=Emacs like Web Browser
GenericName=Web Browser
Exec=conkeror %u
Categories=GNOME;GTK;Network;WebBrowser;
MimeType=text/html;text/xml;application/xhtml+xml;application/xml;application/vnd.mozilla.xul+xml;application/rss+xml;application/rdf+xml;image/gif;image/jpeg;image/png;x-scheme-handler/http;x-scheme-handler/https;x-scheme-handler/ftp;x-scheme-handler/chrome;video/webm;
Conkeror was installed from apt-get by adding this PPA:
sudo apt-add-repository ppa:xtaran/conkeror
Once that's all set, run this command to trick Gnome into using your local firefox.desktop. It'll think it's running Firefox (it is remarkably stubborn about insisting on Firefox) but will run your command instead:
update-desktop-database ~/.local/share/applications gnome-default-applications-properties