One of the toughest parts of note taking systems can be moving from one to another, particularly digital ones, as the technical overhead is almost never easy and typically requires a huge amount of work. Wouter's description here may seem facile, but I'm sure it wasn't simple, not to mention the fact that he's got more facility with coding than the average person ever will.
I do like the idea of basic text or markdown files that can be used in a variety of settings with relatively easy wiki mark up.
Of the systems I've seen, this seems to be the most portable format, but it also requires software that supports it at the base level, but which still provides search and other useful functionalities.