Having been an Evolution user since a few years back, I recently migrated to thunderbird and had a few "problems". Thanks to iolanda I was able to fix most of them. I post my thunderbird setup here, so I can remember when I need to setup it again.
Config Editor Settings
Always keep threads, also when changing sort preferences:
By default sort everything threaded descending by date:
mailnews.default_sort_type=22 (22 is threaded, 18 is date)
(1 is ascending, 2 is descending) ---
there seems to be a bug here, setting it to 2 does not work and slows down thunderbird!
Do not arrange threads by subject (look at msgid, references, in-reply-to, etc.):
Check mail in all folders:
1) [Dictionary switcher](https://addons.mozilla.org/en-US/thunderbird/addon/3993)
2) [Disable drag and drop in the folder pane](https://addons.mozilla.org/en-US/thunderbird/addon/4591) (prevents accidentally moving folders)
3) [FolderCheck](https://addons.mozilla.org/en-US/thunderbird/addon/4936) (only useful if you don't enable check mail in all folders).
4) [Header Scroll extension](https://addons.mozilla.org/en-US/thunderbird/addon/1003)
5) [LookOut](https://addons.mozilla.org/en-US/thunderbird/addon/4433) (decode winmail.dat attachments)
6) [Sync On Arrival](https://addons.mozilla.org/en-US/thunderbird/addon/1396) (Downloads new message headers immediately when there are new messages in a folder)
7) [ThreadBubble](https://addons.mozilla.org/en-US/thunderbird/addon/5326) (resort the threaded view by date when new mail arrives)
8) [View Headers Toggle Button](https://addons.mozilla.org/en-US/thunderbird/addon/210)
9) [ThreadKey](https://addons.mozilla.org/en-US/thunderbird/addon/2299) (Use T/U keys to switch between threaded and unthreaded views).
10) [Enigmail](https://addons.mozilla.org/en-US/thunderbird/addon/71) (Sign and Encrypt/Decrypt emails using GPG)
11)[SmtpSelect](https://addons.mozilla.org/en-US/thunderbird/addon/2234) (Switch SMTP server quickly)