I agree with the comments here, and wholeheartedly recommend Simple Machines Forum (SMF) as software. I'm not affiliated with them, but I've both run and used sites with this forum software. It's great, and it's free!

Just sort of a neophyte here and I'm sure there's some logic behind your format, but I'll try to get a handle on it. Seems like a possible way to allow conversations to evolve more openly, however at the same time I'm not used to creating a new "subject" for every comment. If you're responding to a specific comment wouldn't the subject be the same subject as the comment you're responding to? Here's a format that I like, and It's never stopped me from going off on wild tangents to get my point across.
http://controlcongress.com/

I got a beef with the forums!

Now that the conversations are becoming more intricate and detailed, and crowded, its hard to follow some of them because of the way comments are layered when a person chooses to respond to a specific topic, rather than appearing at the top or bottom of a thread depending on your settings, new posts can pop up in the middle of a thread, and you might have to review 3 or 4 pages of material before finding new posts. Its messy.

Kudos on trying something different and all that, but I believe a QUOTE feature, and a linear posting system would be best.

I don't have technical suggestions because I'm pretty strictly a computer user, I dont know about design or programming or any of that stuff. But I can give you links to forum systems that i have enjoyed in the past if that would help.

vBulletin is a staple almost anywhere you go.

Ikonboards are not so pretty but pretty damn functional.

I have never used but have just seen phpbb boards for the first time while running a web search. Again, its not so pretty but its free.

IPB is also an option that comes to mind.

i personally think vBulletin is the best way to go, but its so over done, they are everywhere, and everywhere its the same sht with a different color scheme.

In the end even myspaces message boards are much more user friendly.

If you put a noose around the neck of a neo con and put him up on a stool, he'll kick the stool out from under himself because "well for better or for worse I'm already here."

The responses are stacked on top of each other at full length, navigating a popular subject is also a bear. Please fix the forums!