> I would love to see comments in a side bar
This is brilliant. A neat way to bootstrap getting this sort of thing implemented in most code editors would be to write a plugin that can do this for existing code and make it good enough to turn heads. It would extract documentation blocks to be presented as prose in a vertically split pane to the right and present the file itself with those blocks hidden—as if automatic folding were turned on. It could even apply some fairly simple heuristics to automatically link to other relevant comments. The goal should be an experience indistinguishable from an embedded iframe showing human-generated API docs from the Web.
Another thing I'd like to kill is the file tree that you see in most VCS Web frontends that tell you the last commit message that touched the file/directory, rather than about the structure of the code.
Netscape's old Bonsai tool tried to do something like this. (When Netscape open sourced Mozilla, they also opened up a lot of their internal tools. This is where Bugzilla came from, but there were others, too.) When you were looking at a directory listing, if the file contained what looked like a short description of its purpose in the comments near the top of the file, Bonsai would grab description and present alongside the file name.
In my own projects today, I try to always include a file overview containing a short, single line description and then write a paragraph or two going into further detail, documenting the whys of the code, and generally explaining its overall role in the project/justifying its existence. I'm basically writing for a tool that doesn't exist but that I'd like to see get created and gain widespread acceptance.