Leading VC blogger Fred Wilson posted some advantages of the Disqus comment plug-in that his firm invested in (based on his usage on the blog!):

1) Threaded discussions

2a) Email Replies

2b) Email Replies for Commenters

3) Shared profiles

(Read the post for details.)

In the comments, Abe Murray noted some missing features that are a showstopper for him:

1. Trackbacks. a huge deal, and totally missing.

2. Seamless data portability. Grab all wordpress / blogger comments on setup and create the Disqus comments for these. If I want to leave Disqus, create wordpress / blogger comments so my blog is still complete.

You should win users by being the best, not by being sticky.

Another commenter ("Andy C") linked to his April 9 post of 25 reasons you should use disqus.

Douglas Karr raised an even bigger showstopper in a comment to that post:

One GIANT REASON not to use Disqus: Your site isn't able to capitalize on User generated content since the comments are loaded via JavaScript. Commenting is a powerful tool for search engines - and you're missing all of it!

Now - if someone builds some robust API blog integration where the comments are loaded server-side, that may make up all the difference. For now, though, DISQUS is hurting blogs by hiding this priceless content from the engines

Despite these issues, the plug-in seems to be gaining plenty of converts.

We covered some alternative comment systems back in September: SezWho, BigSwerve, coComment, Co.mments and Intense Debate.