What I don't like about Thunderbird is the mbox mail format (one file per folder). It's not a good fit for my use case — personal email where some folders can amass many thousands of messages — Thunderbird bogs down eventually.

I've been using Claws Mail, it's fast and customizable, with great filtering and scripting abilities and tray notification plugin included. Claws uses MH format which is one file per message. But it doesn't support maildir.

Evolution is another good client with the ability to use either mbox or maildir, but it stores the metadata in its own format.

mutt is the absolute best if you don't mind a console client.

I heard good things about Balsa but last time I tried it (years ago) it was still not mature.