To clarify, your @reply won't necessarily appear in everyone's feed. It will only appear if:
1) They are the user you are sending the @reply to, OR
2) They follow you AND the person you send the @reply to.
So for example, if I follow @balsamiq and @fogbugz and @balsamiq sends an @reply to @fogbugz, that message will appear in my feed. But if @balsamiq sends an @reply to a user I do not follow, I will not see it in my feed.
Extra tidbit: this is the reason for those ". @foo ..." tweets you may be seeing. If any character precedes the @, then the tweet will appear in all your follower's feeds; otherwise, it behave as jsb described.
1) They are the user you are sending the @reply to, OR 2) They follow you AND the person you send the @reply to.
So for example, if I follow @balsamiq and @fogbugz and @balsamiq sends an @reply to @fogbugz, that message will appear in my feed. But if @balsamiq sends an @reply to a user I do not follow, I will not see it in my feed.