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.
That's a pretty nifty idea. I frequently use email as my todo list (though I really shouldn't...I've been trying to do the email zero thing, but I'm back up to 1000 or so messages in my box again, two weeks after starting).
I do use email as my TODO list, but I publish the length of the queue for all to see. Makes me deal with stuff just knowing that anyone could be looking.
I do just that with mutt. To add notes to an email hit 'e' and it fires up the raw email in emacs (or your favorite editor). Just add comments and save it.
Mutt doesn't have a fancy UI but it is fast. It has no problem handling the 150k+ in my inbox (mostly unread). I know some people that swear by pine and for all the same reasons. YMMV.
If you're stuck on Windows Outlook lets you edit any message (and you can have what you write be in a different color). It was a neat trick I used a couple of years ago.
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.