Just a thought.

but what happens to the threaded list stuff at the top?

Well in IE at 800x600 it's a complete mess anyway, so going to multiple pages solves this problem as well. You could order the list by colour or by connecting lines to show how 'deep' a particular message is, then just have the first post on a new page displayed at the appropriate depth (so it would have the right colour or be indented by the correct number of vertical lines, depending on the method chosen).

The way the system's working right now, however, the 'depth' of the messege isn't really telling anyone anything because to enter a message most people just reply to the last post - giving the meaningless diagonal slant of posts in the list.
There should be a 'post to this thread' button at the bottom of the page, with 'reply to' reserved for when people really need to quote a previous message. Not ideal, but at least depth can start to indicate something.

Oh, and newest pages should be displayed first, or there should at least be an option of reversing the order of posts so you can quickly read the most recent post.

but what happens to the threaded list stuff at the top?

Well in IE at 800x600 it's a complete mess anyway, so going to multiple pages solves this problem as well. You could order the list by colour or by connecting lines to show how 'deep' a particular message is, then just have the first post on a new page displayed at the appropriate depth (so it would have the right colour or be indented by the correct number of vertical lines, depending on the method chosen).

That wouldn't work as the actual messages are listed in date order (changing this isn't an option), so if the 60th message was a reply to the original post then the 'top' post on the 2nd page (or whatever) would have to be indented a lot anyway.

The way the system's working right now, however, the 'depth' of the messege isn't really telling anyone anything because to enter a message most people just reply to the last post - giving the meaningless diagonal slant of posts in the list.

There is that, but some people are using it properly.

There should be a 'post to this thread' button at the bottom of the page, with 'reply to' reserved for when people really need to quote a previous message.

How would these 'reply to' messages appear on the threaded list?

Oh, and newest pages should be displayed first, or there should at least be an option of reversing the order of posts so you can quickly read the most recent post.

Okay. I'll probably end up implementing something like vBulletin where you can click on a link to take you straight to the oldest post since your last visit.