You don't have to unblock Facebook to use most comment sections. More of the major new sites are using either Disqus or a site-specific instance of LiveFyre than are using Facebook Comments as their enhanced commenting platform. USA Today is probably the biggest site using Facebook Comments. A lot of local news stations and small-town papers have moved to Facebook Comments. Lots of blogs and special interest websites now use Disqus to get into that cross-web "discoverability" of their sites by being on the same comment platform as CNN, The Atlantic, etc. Some sites still use Intense Debate, though it's dropped off bigtime. Wonkette probably the biggest political commentary site still using it, some blogs, some small news sites. (Intense Debate had the "early mover disadvantage" - LiveFyre and Disqus are just much better.)
Even for the Facebook Comments-powered sites, you don't have to unblock Facebook globally, if you use the right tool.
Problem: You don't want to be tracked by Facebook all over creation, but you do want to be able to comment on the majority of sites. Including, if they use Facebook comments, those sites.
Solution: Use Ghostery (and I'm specifically recommending Ghostery, not alternatives like Disconnect; I explain why further in) with its fine granularity of global and site-specific blocking.
1. Turn off GhostRank, so you're not telling Evidon (Ghostery) who you're going to. It's off by default so they're being good guys.
2. Turn on auto-update and auto-block new elements.
3. Block everything. (It's just easier to start from blocking everything. 3 after 2 because sometimes first-use leaves stuff unblocked)
4. If you're a regular commenter and comment reader at major sites, unblock the "3pes" (Third Party Tracking Elements) for:
If using the Firefox version of Ghostery, there's a Cookie tab. Repeat steps 3 and 4 on the Cookie tab.
Disqus and Intense Debate have cookies on their list, too, LiveFyre currently does not.)
5. Save (one save covers all the tab settings you've jumped between.)
Do not unblock Facebook or anything with Facebook in it here at the global level. You don't want Facebook knowing every site you've been at that has a Like or Follow button or a Facebook Social Reader app, just the ones you intend to actually read Facebook-powered comments at.
The last several versions of Ghostery for Firefox, and the most recent version for Chrome finally, have per-site per-tracker disabling. So go to the site where you can't see the comments. Click the Ghostery toolbar icon to see the list of trackers blocked. Don't whitelist the whole site. Next to each active tracker, Ghostery has a slide switch. You can unblock Facebook Connect or Facebook Social Graph or whatever you need, just for that site, then reload.
It may well turn iterative. For Facebook comments it certainly will. On USA Today, for example, if you click the little dialog bubble icon on the left panel from the story (which is their comment icon), Ghostery will increment by at least one more tracker, USAtoday didn't load the FB stuff till then. Unblock that and reload, you still won't get the comments. By unblocking Facebook Connect, now it could load Facebook Social Plugins. Now unblock that. Rinse and repeat.
I'm a pretty avid Disqus commenter and have it on all my and my clients' sites, so I leave it unblocked globally. But you could do the same with that, if you only want it to work at certain sites and don't want it knowing you're there at other Disqus-powered sites.
In some cases it may just be sloppy design or bad coding. But it happens enough, and requires enough iterations of "now unblock THAT tracker" on some sites, that I suspect it is privacy-tools-savvy design decisions specifically to thwart people using privacy tools, to force us into unblocking everything in order to get to the comments. (I'm looking at you, Salon.com).
Shouldn't need to be explained, but just in case: You of course have to stop using EasyPrivacy or Fanboy's Social Annoyances or any other list in Adblock Edge (good), Adblock Plus (now evil) or AdBlock for Chrome (good), because that has no per-site per-tracker granularity. Discontinue using your adblocker as your privacy blocker and go back to the basic EasyList (or other list of choice) block list targeting only adverts, not trackers and social. Same thing if you're using a customized hosts file. Don't do that. You have a better tool once you install one of the privacy blocking extension.
Ghostery for IE does exist but doesn't have most of the flexibility of Ghostery for Chrome or Firefox. Plus, IE. I suspect no one here is using it for their own routine browsing, only for special cases or client projects validation. Disconnect is pretty nice, easier to set up than Ghostery (not that that's hard), but doesn't have quite as much per-site granularity. Until the recent Chrome version of Ghostery came out with the same per-site per-tracker controls as the Firefox version, I did prefer Disconnect for Chrome over Ghostery, but no longer.
BlueHell Firewall (misleading term "firewall") for Firefox Mobile is better than a stick in the eye if running/attempting to run Firefox Mobile on a lower-resource Android device. Doesn't have any granular control, just on or off. But it does let you run mobile Firefox with a privacy tracker on phones or tablets that can run Firefox but cramp up and die when you add a heavy extension like Ghostery. If you've got enough processor and memory to run mobile Firefox well, you can use Ghostery successfully, in my experience.