I have been running Thunderbird since about v0.3 and it is generally good but has taken a while to get itself together.
I tried the spam filtering and found it useless. I marked messages for weeks without anything happening and then it suddenly started dumping *everything*. I now have SBL+XBL on the mail server and get a couple of spam messages a day so I don't really need run anything client side any more.
Before 0.8 I used to combine my POP3 folders by setting a rule that said "if the subject isn't 'flibble' move the message to Local Inbox".
Gareth