I've always wanted to be able to write notes on top of emails I receive. So say I receive an email about a new bug, I could just jot down more details into another layer on top that email in transparent font/colour. I've noticed other people often print out emails and do something like this with a red marker.

I use Thunderbird and I've thought about digging around in the source to see if this is possible. It's not something I've found time to do though.