Over the past few months, I've seen what seems like a literal flood of articles comparing various note taking applications. I have no illusions that most of the people involved will ever hear my voice, but I stand by three related principles in choosing for my own use.
They must support open formats that are based on plain text. If the tools for every markup language ever created disappear over the coming years, every file I've written in them will remain readable with any text editor.
Open source tools must be available. There is no guarantee that any given closed source tool will still be available, or that future versions of it will still support reading my "legacy" files. If it's open source, even if I do nothing else with it, I can compile it for newer operating systems and continue to run it.
Finally, reading and writing notes must be distinct from synchronization mechanisms. I want a local copy that I will always have control of. If my data is trapped within someone else's walled garden, I can lose control of it.
The oldest file on my laptop is my .emacs file. There are parts of it that date back to my earliest use of Emacs in about 1988. Any other files that approach that age are also text files of one kind or another. Text editors, command line tools, and every source control system I've ever used are well suited to dealing with text. I trust it because I have decades of proof that I can expect it to still be usable when I need it.