If you had some sort of standard with various different native clients, then it might work.
As in Gmail?
As cookingrobot says, gmails threading is one dimensional and super clunky when you have lots of replies. It auto collapses to far so you can't easily reply to a particular message in the thread.
Reddit has the best comment threading system of any site online. Quora is near the worst. HN is just slightly frustrating.
Reddit used be written in Lisp, but they switched to Python early on: http://blog.reddit.com/2005/12/on-lisp.html
I do agree that they look alike, Hacker News was inspired by Reddit.
No one seems to get this, not HN, not Quora, Digg (though that doesn't matter any longer...)
Its about increasing the information consumption rate and navigation rate. Collapsing is critical to navigating threads with thousands of comments, even tens of comments!
Any UX designer who does not see this, is, in my book, worthless.
> you can't reply to one person's comment
You can, but it doesn't maintain proper threading. It just groups them all together and sorts by date.
Each headline being the suvject being an email with all the comments being the replies. Different users can reply in a threaded way to all the recipients of the message etc.
Obviously it would need in-line attachements and in-line pictures.
It would be interesting to allow a vote system on messages. Rather than file them, you down or up vote them. But in your box, you have more than one vote so you can apply more or less weight to info. Along with tags and groups and many other things that I can think of...
That would be cool.