DevonThinkProOffice shows potential for an Evernote replacement. I’m having good luck with BitTorrentSync for folder syncing. It’s free, and it syncs folders without using the cloud. You install the software, make a user account, and point to a folder that you want to sync. You install and sign up on another machine, and Sync will copy the folder over. Once the initial sync is done, it will keep the folder synced very quickly using peer-to-peer.
I haven’t tried using BTSync with DevonThink yet, but it has real potential.
Zengobi, which makes the world’s greatest creative software – Curio has just started developing a free app with aspirations to be an Evernote killer. it’s called Curiota, and it’s shaping up pretty well. Curiota stores all your data as standard files in non-proprietary formats. It doesn’t even store them in a database – it puts them in Finder folders and uses Spotlight to search. Because it’s just a file tree, BTSync should have no trouble syncing it.
It doesn’t have the big pro features yet, but the developer seems very eager to make it work. Have a look.