Your own site, work, or vendor / client sites could be added.
Or you could want to remove a Comodo (or Honest Achmed's Used Cars and Certificates).
http://www.livehacking.com/2011/04/25/honest-achmeds-used-ca...
https://bugzilla.mozilla.org/show_bug.cgi?id=647959
Just because your OS / browser vendor "trusts" a cert doesn't mean you should.
In other words, users should always have the right to control who they (indirectly) trust. That's what the comment above is referring to - it will be even worse if Superfish is used as an excuse to take away this right.
I presume 'nugget is talking about the HTML rewriting aspect of the software. Injecting additional/unwanted tracking code == bad, user-requested re-writing of content == good.
Very annoying if you wish to use your own CA or add another and it is also dangerous in that it masks any cert installation by malware.
Also if you want to use http://www.cacert.org/ you need to add their cert.