Spectacu.la Discussion adds threaded commenting with live AJAX comments to almost any WordPress Theme.
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.