Open Source/Free Software includes a number of tribes. There are the FSF true believers, epitomized by RMS, who hold that software should be free on philosophical/ideological grounds. Even if one could adduce facts showing that Free Software was less optimal than closed source, these folks would be unmoved; it's a matter of morality.
Then there are folks like Cory Doctorow and ESR who still insist on using strictly Open Software but do so on (mostly) pragmatic grounds. Members of this tribe seek to avoid lock-in or loss of data. It's easy to see why someone like Doctorow would fear having his data locked in some proprietary format that could become unsupported at the whim of some software company.
There's also the tribe that is willing to use a proprietary program or OS, when necessary, as long as it doesn't involve their data. As a Mac user, I fall into this group. Even though I prefer open source, I'm perfectly happy to enjoy the benefits that OS X brings me but I would never use Word, or Pages (the Mac answer to Word), or Numbers (the Mac spreadsheet). Instead all my data is held as plain text (even, thanks to Org Mode, spreadsheet type data). If OS X were to die tomorrow, my data would be just as useful and accessible on Linux or even Windows.
The key here is that you must never commit any data you care about to anything but plain text. If someone or something requires, say, word documents, you write and maintain it in Org- or Markdown-mode and export it to word as Mark Szepieniec and Christophe-Marie Duquesne outlined for résumés. Most of us know and practice all this no matter which tribe we adhere to.
It turns out, though, that it's a bit more complicated. Jonathan Zdziarski has an interesting post on digital forensics and the threat that closed source poses to it. Most law enforcement agencies use closed source programs to extract data from phones or computers and for other forensic tasks. One problem is that the user has no way of knowing what the programs are doing or how they're massaging the data. This can present legal problems when, for example, the defense insists on auditing the program that produced the data. In the case of breathalyzers, which are also mostly closed source, this has already resulted in DUI dismissals.
It gets worse though. Zdziarski reports that the results these forensic programs produce are often flat out wrong—even made up in some cases. That's an obvious problem no matter which side of law enforcement you're on. If you're the defendant, you might get wrongly convicted. If you're with law enforcement, guilty parties may be erroneously cleared.
Closed source isn't the only problem that Zdziarski describes but it is a large one. We will certainly see cases involving forensics depending on these programs challenged and dismissed. In the mean time, those of us who support open source get to feel smug. Just don't find yourself on the wrong end of a digital forensics investigation.