Basically you're looking at a flattened tree. Anytime you see the lines, those are part of the same conversation sequentially. Once the lines stop, that's a new conversation.

http://i.imgur.com/02mm3YW.png

And an ASCII version:

    Tweet
    -----
    1.0 Reply to tweet
    |
    1.1 Reply to 1.0
    |
    1.2 Reply to 1.1
    ----
    2.0 Reply to tweet
    |
    2.1 Reply to 2.0
    |
    2.2 Reply to 2.1
    ---
    3.0 Reply to tweet

So where does a reply to 1.1 go?

Right where 1.2 is. If you wanted to see the direct responses to that, you'd click on that tweet, and then be looking at a new subthread. It's all predicated on whose message the reply-er clicked the reply button on.

    First Tweet
      Reply 1
      Reply 2 <-- click


    Reply 1
      Reply 1.1
      Reply 1.2

You only see the first two levels of the main tweet you're looking at. The first tweet, its replies, and the immediate children of those replies. Some indenting would make this a lot more intuitive.

That is basically my complaint then. I have 1920 horizontal pixels available, but for some reason twitter is intent on only using a small fraction of that.