What is the best method for handling comments?

I’ve personally stayed away from any external or 3rd party system. Many times commenters are apprehensive about using “another” account or service, esp with recent privacy issues with Facebook, etc. Also, many add bloat and delay page load to run their own scripts, etc and can be harder to style to fit within an existing theme. I would look to use the existing WP comment function, plus Askimet and some .htaccess rules to block out spam.