I think @Dan's suggestion of showing only one comment and its ancestors makes a lot of sense. It allows one to see a message in the context of the conversation that lead up to it without the distraction of irrelevant branches.
Initially a post might be displayed like this:
+-------------------------------+
| The Design of Everyday Things |
| by Don Norman |
| |
| [3 comments]|
+-------------------------------+
Clicking [3 comments] or the pressing the down arrow key would open the first comment beneath the post.
+-------------------------------+
| The Design of Everyday Things |
| by Don Norman |
| |
| |
+-------------------------------+
| 1 of 3 [x]|
| |
|< That's a great book! >|
| |
+-------------------------------+
From this point, you could cycle through all of the comments that were written about the post, using either the arrow buttons or right and left arrow keys. (BTW, whenever I say arrow keys, it's easy to imagine the same with a touchscreen swipe, accelerometer tilt, joystick, trackball, etc.)
Let's say you go right to read the next comment:
+-------------------------------+
| The Design of Everyday Things |
| by Don Norman |
| |
| |
+-------------------------------+
| 2 of 3 [x]|
| |
| I want to read this one. |
|< I've read his other two. >|
| |
| [8 comments]|
+-------------------------------+
At this point, you're on a comment that itself has eight comments. You can go down a level and read those comments.
+-------------------------------+
| The Design of Everyday Things |
| by Don Norman |
| |
| |
+-------------------------------+
| 2 of 3 [x]|
| |
| I want to read this one. |
| I've read his other two. |
| |
+-------------------------------+
| 1 of 8 [x]|
| |
| I enjoyed this one and |
|< Emotional Design. I didn't >|
| know there was a third. |
| |
| [2 comments]|
+-------------------------------+
And so on. In theory, it would be easy to follow all of the branches (or just the interesting ones) without running out of space, zooming in and out like a yo-yo, trying to keep the conversation stack in your head, or forgetting what branches have already been visited.
It would also be trivial to save, bookmark, or print a particular comment; its context would automatically be included.