I'm actively looking for a replacement. I have tried Paperwork[2], Laverna[3], and DevonThink[4]
If you're on OSX, and open to a fair amount of upfront work, DevonThink is the best alternative I've used, and can sync with webDAV against Owncloud-or-other-DAV-server for multi-client-access.
That said, I've not yet found anything that approaches the overall feature set of Evernote across OSX+iOS, and continue to use it daily. I wish they would just let us host our notebooks on our own datastores.
[1] https://news.ycombinator.com/item?id=9206002
[4] http://www.devontechnologies.com/products/devonthink/overvie...
Keepnote (Linux/Windows/Mac but awful. I love it on Linux/Windows) http://keepnote.org/
Quiver (Mac) http://happenapps.com/#quiver
Yojimbo (Mac/iOS) http://www.barebones.com/products/yojimbo/
NVAlt (Mac) http://brettterpstra.com/projects/nvalt/
OneNote for Windows (not open format, but can export into open format. Avoid saving notebooks to OneDrive, save them to local disk storage. OneNote for other platforms does not support local storage at all)
ResophNotes (Windows) Aims to be an NVAlt clone. I don't like it, but many others do. http://www.resoph.com/ResophNotes/Welcome.html
I use pocket git and IA writer on Android. It's a great combo!