From the howto at: http://gnome-hacks.jodrell.net/hacks.html?id=11

using Gnome >= 2.2.2 add the following
protocol handler:
(on Fedora in Preferences, Control Panel, File Types)
Add Service under 'Internet Services' and create a new service as
follows:

Description: Mailto Handler
Protocol:    mailto
Program:     yournewscript.sh "%s"

Now it should work.

This was already available to windows systems thanks to cw

It now works with gnome and phpgw 0.9.16 (and likely kde)

First you need to get the home.php from the HEAD branch.  You can download it here .. http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/phpgroupware/phpgroupware/home.php?rev=1.16.2.1.2.5

Next you need to modify your email/inc/bocompose.inc.php.
change (around line 660):
                                if ($mailto)
                                {
                                        $to_box_value = substr($mailto, 7,
strlen($mailto));
                                }


to:
                                if ($mailto)
                                {
                                        $array=parse_url($mailto);
                                        $to_box_value = $array['path'];
                                        parse_str($array['query']);
                                }

Next you use this bash script.
#!/bin/sh
                                                                               
                             
# use a phpgw web mail as a mailto handler
#
# In fedora, go to Menu, Preferences, File Types and Programs
# click on internet and then "Add a service"
# in the run box fill in this script's filename (and path) and then "%s"
# (like /home/scripts/phpgwmailto.sh "%s")
# (there might be a similar way in KDE)
# then edit this file to change the path to galeon (might also work with other
browsers)
# also change the url to your phpgw install

process=`echo $1 | sed 's/%/%25/g
s/ /%20/g
s/      /%09/g
s/!/%21/g
s/"/%22/g
s/#/%23/g
s/\\$/%24/g
s/\&/%26/g
s/'\''/%27/g
s/(/%28/g
s/)/%29/g
s/\*/%2a/g
s/+/%2b/g
s/,/%2c/g
s/-/%2d/g
s/\./%2e/g
s/\//%2f/g
s/:/%3a/g
s/;/%3b/g
s/</%3c/g
s/\=/%3d/g
s/>/%3e/g
s/?/%3f/g
s/@/%40/g
s/\[/%5b/g
s/\\\/%5c/g
s/\]/%5d/g
s/\^/%5e/g
s/_/%5f/g
s/\`/%60/g
s/{/%7b/g
s/|/%7c/g
s/}/%7d/g
s/~/%7e/g'`

/usr/bin/galeon
"http://your.domain.com/phpgroupware/login.php?phpgw_forward=/index.php&phpgw_m
enuaction=email.uicompose.compose&phpgw_mailto=$process"

exit 1