For Amie, and whoever else would need it.
To reply to a tweet on the web, hover over the tweet with your mouse. On the right, you will see a star (to favorite, I think, a tweet?) and a curvy arrow thingie (just above the "reply to Amie31 -- when I took the screenshot, it ignored my mouse cursor).
Click the curvy arrow thingie, and the box at the top that normally looks like this:will change to this:
Et voila, an @reply. :-)
In semi-related news, if you've been following my tweets, you know that I'm looking for my wayward karma. I'd say today trends to neutral, but I haven't tried to burn my News-2-You video yet (since I left my phone and iPod at school...I rock 8-/).