What are the common pitfalls when choosing a note taking application or platform?

Own your data

Prefer note taking systems that don't rely on a company's long term existence. While Evernote or OneNote have been around for a while, there's nothing to say they'll be around forever or even your entire lifetime. That shiny new startup note taking company may not gain traction in the market and exist in two years. If your notes are trapped inside a company's infrastructure and aren't exportable to another location, you're simply dead in the water. Make sure you have a method to be able to export and own the raw data of your notes.

Test driving many

and not choosing or sticking with one (or even a few)<br /> Don't get stunned into inaction by the number of choices.

Shiny object syndrome

is the situation where people focus all attention on something that is new, current or trendy, yet drop this as soon as something new takes its place.<br /> There will always be new and perhaps interesting note taking applications. Some may look fun and you'll be tempted to try them out and fragment your notes. Don't waste your time unless the benefits are manifestly clear and the pathway to exporting your notes is simple and easy. Otherwise you'll spend all your time importing/exporting and managing your notes and not taking and using them. Paper and pencil has been around for centuries and they work, so at a minimum do this. True innovation in this space is exceedingly rare, and even small affordances like the ability to have [[wikilinks]] and/or bi-directional links may save a few seconds here and there, in the long run these can still be done manually and having a system far exceeds the value of having the best system.

(Relate this to the same effect in the blogosphere of people switching CMSes and software and never actually writing content on their website. The purpose of the tool is using it and not collecting all the tools as a distraction for not using them. Remember which problem you're attempting to solve.)

Future needs and whataboutisms

Surely there will be future innovations in the note taking space or you may find some niche need that your current system doesn't solve. Given the maturity of the space even in a pen and paper world, this will be rare. Don't worry inordinately about the future, imitate what has worked for large numbers of people in the past and move forward from there.

Others? Probably...