I use Thunderbird for mail. I use multiple mailboxes to segment my life. I have one that my bosses use to mail me. I have one for some friends. I have one I put on my resumes. I have one (strictly speaking, it's at least 6, potentially more, but one mailbox) that I've been at forever, and it's where most of my mailing lists go, where my parents mail me, and where I can bring the awesome power of Procmail to trigger abstract code through a mail filter. Plus one from my cable company that I don't really use.
Anyway, I use Thunderbird, because it's easier to watch all those mailboxes with one thing than it is to have seventeen windows open. I have Procmail for one mailbox, GMail's server-side sorting for two others, and contempt and Thunderbird's built-in filter for the campus mailbox. So, when I get mail from mailing lists, it goes to the list. When I get spam, for the most part, it gets trashed. Very fine-grained control over what goes where.
And very coarse control over alerts.
I like mailing lists. I'm on a lot, on a few subjects where I'm not the master and not going to be soon. So I collect great gobs of mail and use search functions or grep to find exactly what I'm looking for. But the alert function has just on and off. I don't care if there's a flame war on the opensolaris list, or discussion on new forms of statistical analysis on the Bioconductor list, or a flame war on the guitar list, and the alert function that tells me about that is stealing my focus. What I want is alerts for the people in the office, my parents, my wife, my children, a select set of friends, and complete silence for everyone else.
I'm going to have to write a module, aren't I?