Most websites/web applications today usually require a commenting system as a means to facilitate user interaction with the website to share experiences, opinions, etc. I've been working with Drupal for over 5 years now and have used several commenting system including Drupal's core commenting system, Disqus commenting, Facebook commenting, etc. IMO, the best commenting system for a Drupal website is Disqus. Disqus provides a variety of features that make it easy to use which in turn facilitates better user interaction.
Just scroll to the bottom of this page to see the Disqus commenting section.
Disqus provides integrations with several systems including Facebook, Google, Disqus and Twitter.
Disqus is wonderful at detecting and properly categorizing spam. With Drupal's core commenting system, you would need another module such as Mollum to prevent spam attacks.
The UI provided is very simple to use and understand, yet it includes a wide range of features from comment voting, comment threading, comments on other articles, etc.
Disqus provides both upvoting and downvoting on comments which can be used to rank comments. This allows for higher ranked comments to be viewed atop of the comments listing.
Discus is very popular, it is the most widely utilized commenting platform. The popularity not only means that Disqus is trusted by also that many persons who regularly comment on blogs usually have a Disqus account and is already signed in to Disqus when they land on your page.
One of the Disqus features that I absolutely love is comment moderation, a feature which allow you to set trusted commenters, and moderate comments (whether all comments or a specific type of comments) before they are posted to your website. Disqus also provides mechanisms to allow multiple moderators for a site with different access privileges for each moderator - this is useful for sites that are managed by many people.
Recent Comments Section
Disqus provides a section below the page comments that contains comments on other pages on your website. This section is very useful for bloggers since it may catch the interest of the reader and cause them to browse other articles.