Hi, I use twitter (@bassmanjase), and access it via the website and teh Echofon plugin for Firefox. I've just noticed today that the "in reply to" links no longer appear on the website, but they're still present in Echofon. It's possible that this change happened at the same time as the ReTweet "upgrade" - I saw the popup on my twitter home-page just a couple of days ago.
I thought I'd mention it, since being able to see who someone is replying to is kind of helpful, esp since I have the bit.ly plugin installed which shows the original tweet when I hover over "in reply to". I can't do that any more, since the link is no longer there. There are quite a few users with this problem - just twitter-search "in reply to" and you'll get a decent number of hits. Cheers, Bassmanjase.