How do I have saved email open in Thunderbird on my Mac?

You are suffering from "default application to use" problems. The issue is that Mac OS X, like Windows and just about every other operating system, uses a table of associations to bind a particular file type with a program that can handle it.

For example, double click on a .JPG file and it'll open a different program than a .HTML file or .PPT file will launch. Envision something that's as simple as PPT=PowerPoint, JPG=Preview, HTML=Safari, and so on.

In addition, there's a similar table in your Web browser that associates certain types of links with specific applications or helper plugins or Safari itself. For example, click on a PDF and it might launch the Adobe Acrobat helper app that actually works within Safari (or Firefox, etc), while a different configuration might have Apple's Preview viewer launch as a separate external application.

What you've done when you set your default email program to be Thunderbird is to establish that mapping within your Web browser (for the most part) and for links that start with "mailto:", either explicitly or implicitly. Try it: mailto:help@apple.com.

The problem is, you haven't changed the file binding or mapping. When you save an email message, I'm guessing it has a '.eml' filename suffix and a specific icon that shows up in the Finder and on your Desktop. Am I right?

I use Apple Mail but also have Microsoft Entourage installed on my own computer, so when I drag a message from Apple Mail onto the desktop, here's what I see:

If I drag a message from Entourage, I see the same basic micro-preview icon, but the filename has a '.eml' suffix associated with it.

Either way, the important thing is to see what application is tied to the individual file. You can do this by selecting the file then choosing File --> Get Info... or just pressing Cmd-I. Either way, you'll get to here:

Notice here in the middle that the app that's going to be used is "Mail" (aka Apple Mail). To change it, simply click on the app name in the menu and a list of applications that your Mac thinks can handle this type of file show up:

Pick the one you want - Thunderbird - then click on the "Change All..." button to make it true for all files of this type into the future, not just this individual message.

That's all there is to it. Make sense? I hope so!