How do I set Thunderbird to notify me of new emails in only certain folders?

Solution 1:

  1. Right click on the folder you don't want notifications for;
  2. Select "Properties";
  3. Uncheck the checkbox "When getting new messages for this account, always check this folder".

Solution 2:

2021: Answer now seems to be the Mailbox Alert extension, which allows setting of alerts down to folder level and works in current Thunderbird version as of this message 78.6