First of all, if there is a new reply, it will be bumped back to the top of the very first page of the forum no matter what (save a server error with the dates :wink: ).
For the most part, you shouldn't need to tell someone you've replied. The posts that everyone has a reply in are changed to red text, which lets them easily spot where they've been and off to the side, it says who the last poster is in the Date column which is next to the number of views on the main forum listing. I know I go back to them if I see that my name isn't the last post anymore.
Also, I know a lot of the people here go back through several pages of stuff to get to the point they left of reading on the board, just to make sure they see everything.
However, if you feel you absolutely must let someone know you've made a reply, you can contact them by choosing any of the options they have available at the bottom of their posts (email, ICQ, AIM, YM, etc.), or you can use the Private Messages feature already available on this board. It's in the bunch of links with "Edit Preferences," etc.