I spent a long time looking for my ideal knowledge organizer, and eventually settled on Notecase Pro (http://www.notecasepro.com/).
It's cross-platform, with a functional free version. I have no problem paying for good, useful software, especially (as in this case) when it's produced by a dedicated individual or small company.
I don't know if I agree that Evernote is overrated, but I personally don't like them for what they did to one of my favorite apps, penultimate (iOS notebook app). I specifically bought that app so I could have my notes always with me. Then Evernote buys the company and makes it so I can only access my notebooks if I am online, or if I pay for a pro version. So I buy something for a specific feature, and they take it away but offer to sell the feature back to me.
It's cross-platform, with a functional free version. I have no problem paying for good, useful software, especially (as in this case) when it's produced by a dedicated individual or small company.
Evernote is overrated...