Script to turn flagged emails into reminders
Well, I got the automator to filter the the flagged mail using the action [Find Mail Item (Message is marked with - flagged)]. But there isn't much you can do with the mail items except have them pop up on Mail using action [Display Mail Messages].

Then I found a script here: https://discussions.apple.com/thread/3435695?start=0&amp;tstart=0
that takes mail and automatically generates reminder from Mail. 

I haven't tried it through myself. But hopefully that gives you a start.