In this post I mention my use of Evernote. I actually started using Evernote because I was moving across the country and didn't want to move boxes and boxes of recipe printouts, so I bought a sheetfed scanner and scanned the paperwork. That was years ago and I invested the time it took to design (figure out) how to classify stuff.
I have hundreds of cookbooks which I read like novels, for entertainment. Others have recommended the site Eat Your Books but it can't answer the questions I want to ask. (I know this because I have repeatedly tested it with my five free books). If I wanted to use Eat Your Books like I use Evernote, I would have to compile custom indeces. If I'm going to compile custom indeces, why do I need Eat Your Books?
So, you have to decide, like @teonzo, how much organization you want. And then you have to put in the effort to achieve it.
The problem is primarily an organizational one.