I now feel that 95% of bloggers should switch to using Disqus, though I have some reservations.

These are some of the reasons why:-

• Matt Cutts today confirmed that nofollow links can reduce the amount of PageRank that flow to internal pages. The easiest current solution to solve this problem is to use Javascript for comments.
  It is an external javascript file, which Google can’t really handle currently, and even if they did, the chances are it might only count as a single link to your disqus discussion.
  Blogstorm has gone into the problems facing comment links in more detail, something I highlighted when Matt first mentioned this clarification at SMX.
• Matt Cutts in the same post highlighted again who you link to matters, and I think Google is going to place more and more emphasis on this. It is a lot of work for the average blogger to keep control of user generated content, and even the best comments sometimes come with spammy links. I have always maintained that “dofollow” isn’t for everyone because of the time commitment.
• Disqus is universal – it can be installed on every major blogging platform – many SEO solutions won’t be universal or easy to implement
• Can Spam & Email Deliverability – this is 50/50 – I have highlighted in the past that emails being sent from your own domain can be a significant liability
  

  It is your choice based on your own research and the legal advice you have received whether you think emails being sent from your domain which are not totally under your control could represent a problem.
  I honestly don’t know if Safe Harbour rules might apply to email delivery. I don’t know of any blog owner who has had problems either from a legal perspective, or with their hosting or domain registrars, but then I personally only know a few people who have been killed in car accidents – I know a lot more people who drive cars than publish business blogs.

• Invalidated Cache – this is a major consideration for high traffic blogs, and potentially product launches. The javascript doesn’t change on each new page load, thus your cached content also doesn’t change (if you just use their javascript on your page) – this can represent a major reduction in server load, even if you are using some kind of Op Cache (eaccelerator APC Xcache), RAM based page cache (Memcached) or more advanced techniques using page chunking. Forget conventional WP Cache / Supercache for product launches, it just can’t cope on its own.
• Social Media Viral Effect – the social media viral effect of using Discus is significant. Not many people are exposed to services such as backtype, but tons of people use Facebook – implementation of Facebook, Twitter and other logins for commenting whilst possible with WordPress isn’t trivial, and that is more plugins to deal with, more server load etc.
• Get to visit Disqus more often – I sometimes leave comments on other blogs that are using Disqus, and sometimes the comment notifications don’t get to me (deliverability issues) – I just noticed on my Andy Beard Disqus profile that Scott Rafer responded to something important 2 months ago, and I didn’t see it.

Negative Side of Disqus

• The SEO of the site needs some major work – it is almost insulting that the link to Twitter on my Disqus profile is followed, yet the link to my blog isn’t. The anchor text from a conversation on Disqus back to a blog isn’t exactly ideal. This is how Google sees my Discus Profile
• Google is very bad at indexing content on Disqus – this is partially due to the Disqus SEO problems – certainly a conversation I took part in 4 days ago isn’t indexed.
• I have heard reports that managing spam can be an issue, though I haven’t tested it, I rarely see spam on highly popular blogs
• It isn’t suitable for private content – you would have to use alternative commenting on private posts if you are running your blog as a membership site. That is something that can be worked around.
• It is hard, maybe impossible to market to people after they have left a comment. With standard WordPress comments, after someone has left an email, you could present a page offering site membership, a one time offer, or an affiliate product – even suggest related content of interest.
• If you have lots of niche blogs, you will hardly want to include all of them on a single Disqus profile if you want to stay under the radar of your competitors. How would a blog network cope? Retain ownership? I can’t see B5 Network with a profile of 300+ blogs in Disqus and managing who can moderate comments.

The SEO problems with Disqus are fixable, and in the current Google climate could offer significant advantages – plus Disqus could conservatively gain at least 400% traffic even without new adoption.
It is possible even if they also gave much more SEO friendly links throughout the whole site.

I am recommending Disqus above competitors JSKit and Intense Debate because both of these services the email subscriptions don’t stack in Gmail – a nightmare if you subscribe to comments on a popular blog, plus I believe there is more chance of Disqus fixing problems for a win/win solution.

Who knows, we might even get Twitter to remove nofollows too… eventually

Disclosure:- I am recommending Disqus even though part of my startup plans would have involved an SEO, product launch and membership friendly system with refined marketing funnel. If I ever get it off the ground, there are ways to migrate back from Disqus.