I have a protected Twitter account. If I reply to a tweet from somebody I'm following, and they're not following me, will they see the reply?
They will not - taken from the What are @Replies section from the Twitter FAQ
Please note that if your account is private, users who are not following you will not see your @replies or mentions.
Yes, they can. They cannot view your protected tweets directly on twitter, but they can view your tweets through topsy.com