Derek Sivers suggests, in a much-linked-to post , that all your stuff should be in plain text files, and I (almost) agree with him.
Most of my notes are in some form of plain text format, but not for the reasons Sivers lists. My notes are in plain text because I prefer editors that use plain text by default. I suggest you use the tools and formats that are most useful to you now. If that’s plain text, then great.
The fear of not being able to open or otherwise read files, someday in the future, is overblown. File formats last a long time. Email, PDF, even Word documents can be opened decades later. Mine can, anyway. But what about in 100 or 200 years? My response is, “Who cares?” I mean, c’mon. My digital notes are going to be tossed in a dumpster along with the rest of my shit by my family like 20 minutes after I die, anyway. Your notes may be more important to the world than mine.
The thing I worry about isn’t “lock-in” or lack of portability or any of those. What I worry about is losing the actual files. This happened to me recently. I try to keep methodical backups, but I was careless with a folder full of Markdown files that were used to render a blog and they are all gone. Hundreds of them. I thought I knew where they were and I thought I’d made backups and a combination of cleaning up and switching machines and poof! All gone. Fortunately, I have the rendered HTML files but my point is that, whatever their format, all files are useless if you lose them.
So, back up those Word docs and PDFs and Mindmaps and Powerpoints. And back up your plain text files, too. At least that way you stand a chance of having them “someday in the future”. You can worry about how to open them then.