As Neil tipped me in in the comments to my previous post on the subject, there's a Growl project to integrate it with Thunderbird and Firefox. I finally got a chance to poke at it today, and it seems to work better than my previous setup, in the sense that when it saw my spam folder I just got a small lineup of bubbles on the right hand side of my display - score. I still wish I could have it ignore everything but the actual Inbox altogether though. Not sure if it's an issue with Thunderbird or the plugin.
(Edit: I worked out last night that to get around disasters with the previous setup seeing tons of new messages, you can kill all processes that look like this: /Users/userid/Library/PreferencePanes/Growl.prefPane/Content. The popups will disappear.)