We use Google Apps extensively here at JROX.COM, and I was a bit annoyed that the default mailto: links in Firefox only had the regular GMail option to use for clicking on the mailto: links.
Luckily, I found a pretty cool config setting to register Google Apps as the default email client to use when clicking on those mailto: links.

1. You need to first type in about:config in your Firefox address bar
2. In the filter field, copy and paste the following:
   
   gecko.handlerService.allowRegisterFromDifferentHost
   
   
3. You must then double click that option to set it to true
4. In the address bar, copy and paste the following:
   
   javascript:window.navigator.registerProtocolHandler("mailto","https://mail.google.com/a/yourdomain.com/mail/?extsrc=mailto&url=%s","Google Apps")
   
   
5. Replace “yourdomain.com” with your own Google Apps hosted domain and hit enter
6. Select the Add Application option when Firefox asks you to.
7. Now, in Firefox, click on Tools > Options > Applications and search for the mailto option.
8. Select Google Apps for Gmail.