I know this could be a point of much controversy, but I encourage people to avoid "top quoting" i.e. having a long quote of sometimes the entire email you want to comment on, and then putting comments underneath.

I don't like "bottom quoting" much either, although it does have the advantage that you don't have to scroll a few pages to read the mail... ideally, snip out relevant parts and quote on those. It's probasbly not difficult for most people to go back to the mail being refered to and check, if further depth is needed.