Over the years, the net developed a custom of responding to messages by quoting parts of it, and adding a comment directly after the quote. Someone coming into the middle of a discussion can often just read through a given message as a kind of pseudo-dialog, following the back-and-forth flow of the argument.
(Also, quoting the entire previous message was considered very poor form. Ideally you should only quote the portions you want to respond to. Primarily the reason to trim your quotations is as a courtesy to the reader, though you'll often see people talk about "not wasting bandwidth". But the main problem these days has little to do with bandwith in the sense of disk storage limits -- and maybe it never really did. Mental bandwidth is the important thing.)
When email spread to the corporate world, however, a different style started becoming commonplace. People responded to messages by placing the new material on top, leaving the previous message (usually quoted in it's entirety) tacked on to the bottom. It is possible that this is well suited to a discussion carried out in a business environment, where you can expect everyone involved to read and respond to the mail promptly (because it's part of their jobs). In this case, everyone is carrying the discussion in their head, and the quoted message is just for reference anyway -- it's a little closer to being an actual dialog, conducted in real-time. And there's no point in wasting your time in trimming down the quoted message, because most people won't be looking at it anyway.
Taking this corporate-style out on the net is a very bad idea. Your main audience in this case is not supposed to be the person you're arguing with. There's a much wider audience of people "listening" to the debate, and your style of quoting should reflect that fact. Starting out a message like so:
"Yes, I agree completely with you on the subject of partitions, but there are some other issues to consider about different distributions --"This is really bad form. Most readers are bound to be thrown by this (Huh? What was the other guy saying about partitions? Who is this in response to?). What is the reader supposed to do, scroll down to the bottom to see if you've quoted anything, then skip back to the top to read the response?
And then things get really fun when you have people talking to each other using different styles of quoting. Instead of having a coherent flow, whether chronological or inverse chronological, you get a weird mix jumping around in different ways, depending on who decided to reply when...
http://www.sni.net/~kassj/netiquette.html
Only quote the needed parts and reply directly after the item you wish to respond to...http://www.bgsu.edu/colleges/library/infosrv/lue/internet/email2.html
Don't let your mailing or Usenet software automatically quote the entire body of messages you are replying to when it's not necessary. Take the time to edit any quotations down to the minimum necessary to provide context for your reply.http://online.santarosa.edu/net/email/netiquette.html
Quote back only the smallest amount you need to make your context clear.