Technology changes quickly, incrementally. It's likely that we'll be doing things differently on different kinds of devices in five years. Whatever tools you decide to use today, make sure you'll be able to move materials from one system to another tomorrow.
Look for import and export functions in software you choose. That means if better software comes along or your needs change, you'll be able to move notes and materials from one system to another relatively painlessly and automatically with one click.
Avoid software without these functions.