I've always been taught it's polite to trim emails and type the reply below the text I'm responding to:

    Because it messes up the order in which people normally read text.
    > Why is top-posting such a bad thing?
    >> Top-posting.
    >>> What is the most annoying thing in e-mail?

But technology has changed. Mail readers used to show just a single message, but now they group related messages together. When you need to see the context of a reply you can look up and see past messages. Because you rarely need to look at quoted sections, they can be collapsed by default. [1] Email etiquette is all about being considerate of your reader, but now that tools have caught up with usage, top and bottom posting are equally easy to read.

At this point bottom posting, unless you're responding inline, only serves to signal identity as someone who learned the ways of the old internet. Unfortunately it's a signal that few people will even see.

Update 2013-02-17: Lots of discussion on hn.

[1] Gmail is smart enough to collapse quoted sections only if you've already seen them. If you're added to a conversation in progress they're left in full for you to read.