Because your comments are stored on a central server and not on each individual blog, you only need to go to one place to see if anyone has responded to or "liked" a comment you have made recently across many blogs. Wordpress.com has a similar feature across all Wordpress.com-hosted blogs.
Since your commenting history across many blogs is stored in one place, anyone can click on your name on any comment you've made and see a list of other comments you've made on other blogs. This is not only useful for getting to know blog commenters, but it benefits the owner of a blog by bringing traffic. Say you go and leave some witty comment on a Wired article and another comment on my blog. Everyone that reads your comment on the Wired article and is curious enough to click on your name will then see your comment on my blog and could potentially find my blog.
The way Disqus gives you the open comment box first, and then makes you give your name or log in through some other service, is pure psychological genius. People will be much more willing to give a name and submit a comment if they have already written something than if you ask for a name and email address up front. Just one of many clever user interface insights Disqus employs.
Since your comments are stored on Disqus' servers, you don't have much of a guarantee that they won't just shut down operations and all your comments will be lost. At least when my comments were kept locally on my own blog, I can back them up as I see fit and make sure they are preserved.
First I asked two of my colleagues, James and Cole, who are search engine optimization (SEO) experts, why anyone would accept the loss of comment keywords and choose Disqus. They referred to all the social traffic I listed in the Pros section and guess that the extra traffic from cross-site commenter interest might be worth the loss of keywords.
Still dubious, I began to investigate...and that's when I found the answer: the Disqus Comment System plugin for Wordpress!
This not only lets you stop using Disqus whenever you like, and still have all your comments intact from your time using Disqus, but it totally blows away the SEO issue by displaying your comments on your blog for search engines and then using Disqus' superior interface for human visitors! Both items from the Cons list have been eliminated, leaving me with no other reasonable option other than to switch to Disqus.
I hope you enjoy the change, dear readers. You might want to set up a Disqus profile so you don't have to enter your information with every comment.