Windows, Macintosh: To make Mozilla use another mail program, you can either (a) uninstall Mozilla, then re-install using Browser Only (Mail/News not installed), or (b) add this line to user.js:
user_pref("network.protocol-<B style="color:black;background-color:#A0FFFF">handler</B>.external.<B style="color:black;background-color:#ffff66">mailto</B>", true);
This will open the system default mail program when you click on an e-mail link in Mozilla.
GNOME, KDE (Unix/Linux): This is not yet possible in GNOME or KDE, but work is in progress to make Mozilla for Unix compliant with the X Desktop Group Standard as it is finalized.
An additional option introduced in Mozilla Firefox is the [WebmailCompose] extension which has compatibility with squirrelmail systems already in place. See https://addons.mozilla.org/extensions/moreinfo.php?id=206 for details.