A “show notifications for this folder” option per folder (some mobile email clients take this approach)
Based on some prior conversations, this would be the better approach. The trick is figuring out how to offer the option.
On that note, we have some other related problems that will need solving soon, so however this option is presented would need to be extensible to fit the other situations:
The ideal solution in my view would be to add a context menu to items on the folder/account view on the left pane, so you could check/uncheck “Notify” on accounts and folders. We could later add a “Mute for…” submenu, and perhaps an overall notification control button.