Thanks, Marc - I'll take a look at it, though I'm a little confused by the description, specifically by what you mean by "2nd level thread," since it sounds like you're saying "not every comment on threads at depth 3, 4, etc."
Anyway, adding the reply links is good, and it's cool if you've come up with a way to do it that doesn't require editing or replacing template files, but I was as interested in, and eventually got to, extending threads "infinitely" (or unboundedly), so that really long ones don't jam up confusingly wherever they end - was more of a concern at a busy blog where threaded conversations semi-regularly go into the hundreds of comments.
The code I used in the above is kind of "IRT Classic" - if you search for its constituent parts you'll find them used in a lot of places. It may appear in the Wordpress Codex somewhere, and I wonder if comment_parent wasn't added to WP core for precisely this purpose.
I like your version of IRT via function. In fact, I think I will very soon try a version of it to add IRT links to this blog. Once that's accomplished, it ought to make for a cute little plug-in, assuming there isn't one already in the repo I never noticed. (If you or someone else beats me to the punch, I'll try it out here.)
I'm not sure about Google+ and Facebook for long discussions - either at the sites themselves or in comment threads styled to emulate them - in part because I've never been in or attempted to follow one in such a situation, though I have been in long, un-threaded discussions that eventually became very burdensome to try to develop, since by comment 100 or 200 there may be several discussions going on at once, or threads that have been abandoned because they've just become to difficult to find and follow.
Because the Ordinary Times site has a unique commenter community, featuring a number of intelligent, voluble, and polite yet argumentative souls, many of whom have been discussing political and cultural topics with each other for years now, the comments and sidebar and sidebar-to-the-sidebar discussions sometimes get long and involved, putting more or a premium on whatever enhancements you can think of: My first goal since I started working at OT was doing things that would make my own participation easier.