Thunderbird is a very useful mail application. Since its inception, it lacked the Firefox traction, but when I was forced to use it, I must admit I found it offered all the features you'd expect from a complete e-mail application.
Disable Open Messages on a new "TAB".
Since the latest versions, they acquired the "tabbed" GUI paradigm and applied it to e-mail messages management.
Can I say this is the worst default feature of all times for an email client? Alright, Suffice it to say I just thought it!
Enable per-message windows: "Tools" -> "Options" -> "Advanced" -> "Open New Messages" -> @ON A NEW WINDOW@.
Another (not so) great default "feature" for new Thunderbird versions was the reply. Basically, when you replied to someone, TB attached "the someone's e-mail" as an attachment (honestly this default makes me chunder too...).
Enable in-body reply/forward reply: "Tools" -> "Options" -> "Composing Email Messages" - "Main" -> "Forward Messages" > @ON THE MESSAGE BODY@
The following are 2 simple customizations I did have to apply because they improved my productivity.