Can we get an alert when someone replies to your comment thread?

Yes; just sign up for Notifo, and put your Notifo id in the notifo field of your profile.

YC startup http://notifo.com/ will do this.

edited

Just a thought, if you want to do this then I recommend not posting anything that becomes popular. I wouldn't be happy if I woke up with 100 email notifications that my thread had been replied to.