Changing the default browser in Thunderbird

If you are unable to launch Firefox from URL links in a Thunderbird mail message, or if you want to change the browser that is launched, add the following lines to the user.js file, located in your Thunderbird profile folder (you may need to create the user.js file). Change the path of the Firefox executable, if yours is not /usr/bin/firefox.

user_pref("network.protocol-handler.app.http", "/usr/bin/firefox");  
  
user_pref("network.protocol-handler.app.https", "/usr/bin/firefox");  
  
user_pref("network.protocol-handler.app.ftp", "/usr/bin/firefox");

Note: You can also use about:config to set these preferences. See Register protocol and network.protocol-handler.app.(protocol) for more information.

If you are still unable to change the browser after modifying these settings, editing the mimeTypes.rdf file, also located in your Profile folder, can fix the problem. Simply use a text editor to search for all references to the browser that links are currently opening in and replace them with references to the browser that you would like links to open in.

If there are no references to browsers to be replaced in the mimeTypes.rdf file, then adding some new sections to this file can fix the problem. Rather than directly editing the file, you can get Thunderbird to automatically add the required sections as follows:

• Navigate to “Edit –> Preferences –> Advanced” in the Thunderbird menus and click on the “Config Editor” button.
• Search for the following three entries:
  • network.protocol-handler.warn-external.http
  • network.protocol-handler.warn-external.https
  • network.protocol-handler.warn-external.ftp 
• Set the value of each of these three entries to true (you can do this by double-clicking on each entry, then close the about:config window and click “OK” on the “Thunderbird Preferences” window). 

Having completed these steps, the next time you click on an http, https or ftp link in Thunderbird, you will be presented with the “Launch Application” window. Press the “Choose” button on this window to select your browser of choice. This will add the required entry to the mimeTypes.rdf file. This is a one-time task; having selected the browser once, links of the same type will now always be opened with the selected browser.

source: http://kb.mozillazine.org/Default_browser#Setting_the_browser_that_opens_in_Thunderbird_-_Linux