sascott: I use Thunderbird all the time and used to use (and hopefully will again use) Messenger a lot. I've been trying to think of the answer to your question, and I don't think there is one! Messenger and Thunderbird are just *so* different.
It's hard to think how two programs which perform the same basic function could be more different in fact (at least, to me).
Certainly Messenger has far more features than Thunderbird - with the notable exceptions mentioned by flyingpig. (I have high hopes that the folder situation will be improved in the current development 'spurt' though )