Just an implementation note...I recently spent several hours researching and trying out comment engines. The various hosted systems like YACCS can be quite nice, but when their servers slow down it slowed my site down. There are some nice PHP systems, but that was a learning curve I wanted to avoid. I ended using SnorComments2, a simple little Perl-driven system. Set up was painless, it doesn't require any additional Perl modules, the interface is highly customizable, and it even has its own little admin interface.
Within Tinderbox, I set up a Boolean attribute for notes that let's me turn on comments or not for each note.