I don't do this in emails, but in posts and PMs I reply underneath. In most of my PMs, I don't even include all of the replies sent back and forth, but if I do, I have to post underneath. It's just like a post. When you quote something, and you post underneath it so people know what you're commenting on. I think of that when responding to a PM. It drives me crazy to see the text on top of all the replies.