We get a lot of email here at ShooFlyDesign HQ. A lot. We also write a lot of email. And we prefer our email without the HTML -- which is what allows people to make text bold, colorful, add images and whatnot. We're just plain text folk here.
One of the weird things about HTML messages, and how Apple Mail deals with them, is that they can mess up replies. Specifically, the leading (line spacing) is broken, resulting in lines that are spaced just far enough apart to look funny, but not as far apart as separate paragraphs should be.
Most email messages that come as HTML also feature an alternative, plain text, encoding. It's possible to switch between these using the View > Message > Plain Text Alternative command. Switch to plain text, hit reply, and everything is jolly.
Apple Mail will display HTML mail encodings by default, on the assumption that users prefer that. And these days, it's possible most do -- the kids like the colorful text and stuff. However, if you have a taste in email similar to ours, you may want to force Apple Mail to display the plain text version if it's available. There's a hidden preference available for it. Quit Mail, open a Terminal window, and paste in this line:
defaults write com.apple.mail PreferPlainText -bool TRUE
Restart Mail, and you will always see a plain text version of a message first. For more information on this topic, including ways to force plain text in other email applications, see Why HTML in E-Mail is a Bad Idea, where I found this solution. The page's filename is amusing: evilmail.html -- calling HTML mail evil might be taking it a little far, but we certainly prefer to avoid it.