While searching for an alternative as well I stumbled over this one: Keepmark
It seems to do exactly all the things I liked about Evernote (local notebooks, searching even inside PDFs) and doesn't do the things (cloud syncing, proprietary file format) I didn't like.
It's still in development and it costs 19 EUR but it's a lifetime license and in case it should ever be discontinued you can still use your files afterwards. I'm going to give it a try.
Apart from that I also found Docspell which sounded promising but it seems you have to have experience with Linux if you want to run it.