Yes, it does! Flagging messages as important/unimportant is already supported in the code, but the feature is currently disabled in the UI. I plan to enable it once I add sections support to the Inbox to match up to Gmail's Priority Inbox feature.
On this note, the notifications are popping off about every 10 minutes for me. It would nice if I could set notifications to only show for "important" emails.
PS - Thanks for the app, it's already an improvement in some ways over the gmail interface... looking forward to even more!