A recent doctoral student of mine came up with an interesting tool to help manage revisions to his dissertation in light of comments from ...
I've written it up on my wiki, here, and everyone's welcome to take a look at it.
Basically, it's just a spreadsheet with one row per "examiner concern." Each concern/row has a status cell, and cells for actions and supervisor comments. The biggest bonus for me personally was that it facilitated asynchronous communication with my student so that we weren't forced to meet face-to-face unless the questions raised required it. This greatly helped the student to work at his own pace, yet keep me in the loop on everything - without me having to constantly refer to the dissertation itself.
I found it really streamlined things for me. Maybe it will also help others.