I don't have much experience with these SaaS comment systems, but in terms of SEO the only thing that should have any effect is whether the comments are visible to Google or not, i.e. whether Google treats the comments as more page content or the comments are basically treated as SEO-inert.
I believe Facebook now uses
iframes to embed their comment system. This most-likely means that, though Google might see and crawl the comments, they won't be considered part of the page. So whereas internal commenting systems add additional indexed content to the page, Facebook comments are simply treated as a separate page.
Disqus supposedly renders a plain-text, non-framed version of the comments on the page in a hidden
div. And there's some evidence that this works for most sites. It's technically cloaking, but Google probably won't penalize you for it since the user sees the same thing (just through the
iframe rather than the hidden
Other people have also used OpenGraph to insert Facebook comments directly into the page in a manner similar to Disqus. It's not an ideal system, but since most of these comment systems are embedded via
iframes, it's the only way to make them SEO-friendly.
There are other benefits and drawbacks to various systems, but none of them directly relate to SEO.