I was able to make Firefox 27.0.1 OpenSUSE 12.3 x64 use Squirrelmail for mailto: addresses by carefully following these instructions:
  http://forums.mozillazine.org/viewtopic.php?f=7&t=2399957
  using
https://<your server>/<squirrelmail base dir>/src/mailto.php?emailaddress=%s      (as opposed to %1 in other instructions, and I configured to use https instead of http at my site)

Similarly for Chromium (I haven't tried this one yet):
  https://bbs.archlinux.org/viewtopic.php?id=154031

Making either browser use Squirrelmail for mailto: composition addresses is a challenging/difficult problem.  Firefox has defaults for GMail and Yahoo preconfigured.
  Chromium doesn't appear to have a default mailto: handler.  I couldn't find any straightforward way for a "normal" user (non-programmer) to configure anything as a mailto handler in either browser which isn't already built-in.  As the fellow in the first article said, "Gee, it only took 1.5 years to figure out".  Both browsers have some addons/extensions applications available which can be found by searching for "mailto" in their respective application areas.

While debugging, I pasted the URL
   http://<your server>/<squirrelmail base dir>/src/mailto.php?emailaddress=myEmail@myDomain.com
into my browser of choice to ensure I had the correct URL format.  The rest was getting my browser configured to use the URL I want, and in Firefox, replace myEmail@myDomain.com with %s.

I hope these two articles help you get to where you want to go:
 
http://forums.mozillazine.org/viewtopic.php?f=7&t=2399957
 
https://bbs.archlinux.org/viewtopic.php?id=154031

Craig

On 03/07/2014 08:51 AM, Chris Hodgson wrote:
We are running a number of Linux Thin Client machines (GNOME).  We would 
like to have squirrelmail as the default mailto handler.

I found documentation on the squirrelmail page with regards to this for 
Windows and Mac but not Linux.  I know in Linux there is a spot under 
Preferred Applications to set a Mail Reader.  And below that there is a 
place to put in a command.

I tried using the information from here 
https://squirrelmail.org/docs/stable-code/squirrelmail/_src---mailto.php.html 
But it is still not working.  If someone could put me in the right 
direction that would be great.

As well I know you can change the default handler in Chrome but I do not 
believe squirrelmail is an option.