As lots of the other comments suggest, I think a highly context dependent approach is probably best. If the email is a response within a group of people, I'll assume that everyone has read the prior email or two (or has access to it in their mail reader). In that case, if my message is a single response to the entire content of the message, then I'll top-post, so within their email reader, they can read only the relevant new bits (my message), then go back to the quoted text below for context if they've forgotten.
On the other hand, if there are specific points that I want to address, I will happily interleave my text, to make it especially clear what I'm responding to. As in everything, look at the context, and see what makes the most sense.
In regards to the "sounds great!" response, the OP was just a poor answer to the question, regardless of whether it was above or below. It would be like if I asked you whether you wanted coffee or tea, and you just said "Yes". While technically true in a Boolean sense, it doesn't help me decide which one to pour.
On the other hand, if there are specific points that I want to address, I will happily interleave my text, to make it especially clear what I'm responding to. As in everything, look at the context, and see what makes the most sense.
In regards to the "sounds great!" response, the OP was just a poor answer to the question, regardless of whether it was above or below. It would be like if I asked you whether you wanted coffee or tea, and you just said "Yes". While technically true in a Boolean sense, it doesn't help me decide which one to pour.