Spectacu.la Discussion adds threaded commenting with live AJAX comments to almost any WordPress Theme.
This has been one of my go to's for awhile.
The only reason I'm not giving this "must have" plug-in 5 stars is because (AFAIKT) it lacks a WYSIWYG editor.
The ability to "Quote" and "Reply" to individual posts is excellent, and nesting those replies gets an A+. Overall looks great and nicely formats your comments.
Now if it only the editor had a GUI.