Simple, see the dark blue bar directly above this text? (That says "Re: threaded vs flat" and has the reply link in it) have it indent with a second color. The space for the text stays the same, and the usernames and avatars stay lined up on the left, but the bar would show you how deep into a specific thread you were. It could also automatically adjust when it would otherwise start to get close to the right hand of the screen by reducing the distance the indention covered each time.

Course I don’t know how easy it would be to implement, but it’s an idea........