CL - I do both. For articles I have used email if available, but with too many magazines the writer's guidelines just give an address. For books I try to get an editor interested in the idea by pasting the chapter outline then offer the full proposal which I send by mail.

One thing I have noticed though, when an editor is interested, the email version comes right back within days. If not interested - you get nothing (with one exception where I had a response). For written queries if you send an SAE the likelyhood of at least getting the 'no thank you' note is higher.
This is not a scientific observation though - just my gut feelings.

Katy, I agree with you about the responses. If I send an email query, I only get a response if the publication is interested. Otherwise, it is like dropping a query into a black hole.

While I like the ease and convenience of email queries, I do not like the lack of response. A really quick 'no thanks' would free me up to consider other markets.

Happy

Use a written query with an Email address for the publisher or editor to respond to you. It's human nature to open an envelope but also human nature to use Email as a convenience to answer the letter.

It's less likely your written query will be lost or overlooked when the editor's opens their inbox and reads 'you have 210 new messages'.