This is a bit of a hack, but it should work.

1. Go to about:config (by typing it in the location bar), and click "I'll be careful, I promise!" if it appears.
2. Type in (or copy and paste) gecko.handlerService.schemes.mailto.2 into the filter box.
3. Double-click "gecko.handlerService.schemes.mailto.2.name", type in Google Apps Mail (or something similar), then press OK.
4. Double-click "gecko.handlerService.schemes.mailto.2.uriTemplate", type in https://mail.google.com/a/domain/?extsrc=mailto&url=%s, where domain is your Google Apps domain, then press OK.

You should now be able to click on any email link to send emails via Google Apps.

I researched this and found you have to download and install gmail notifier. After I did this, a pop up window asked for my email address and password that I use for gmail. After you do this, look for the little email symbol in your tray, then select Options, click the box that says, Use Gmail for internet mailto: links, then select the browser you are using. These are: default system, Internet Explorer, Google Chrome and Mozilla Firefox . I selected Firefox, and it works perfectly.

Gmail Notifier

I started by locating the Gmail notifier add-on; when I found it, the page displayed "Not available for Firefox 9.0.1". Absolute bummer! I've used the "Use Gmail for Internet email" with past versions of Firefox, but now it's unavailable. Guess it's a lot to ask for that every add-on gets updated for every release, huh? Oh well! Still love my FF!