This article was first written in March 2005 for the BeezNest technical website (http://glasnost.beeznest.org/articles/213).
Answering under the question should be the default. Similarly, and to avoid complicating answering to e-mails, try to cover only one topic (even huge) per e-mail. It will not cost you more to split your different subjects in several messages, and will allow you to give sensible subjects to your e-mails easily.
In return, you can expect the answers to be more readable and finding something through all your e-mails far faster.