Just because software is highly rated, open source, and generally better than the opposition doesn't mean that it can't be annoying.
Case in point, Firefox. I clicked on a PDF link and got a message which, paraphrased, was:
The file /tmp/foobar.pdf could not be opened because the helper application was not present.
OK, the helper application I used before the upgrade was Acroread. I haven't bothered to load up the binary as yet, so, indeed, it's not present in the system. This should be easy to fix, but when I go to Edit=>Preference=>Content, and click the “Manage” button after “Configure how Firefox handles certain types of files” I don't see PDF files. Even though Firefox admits that there should be an application.
All is not lost, though it's pretty hard to find. To fix this bug,
$ cd ~/.mozilla/firefox/insertyoursetofrandomnumbershere.default $ grep "acroread" *
Which returns, in my case
mimeTypes.rdf: NC:path="/usr/bin/acroread" mimeTypes.rdf: NC:prettyName="acroread" />
Kill Firefox. Edit the mimeTypes.rdf file. In my case I replace acroread by evince, but you can use xpdf or even gv if you like. Restart Firefox. Click on a PDF link. It should come up.
Problem solved, but it's not something I should have to do this way.