Another open-source Evernote alternative is TurtlTurtl, currently in beta -- but more than simply being an alternative, it bills itself as being a secure alternative:
Think of Turtl as Evernote with ultimate privacy.
I learned about it from a recent post on WebUpd8 which included this screenshot:
While in beta, it is "free" to use the Turtl servers, although there is a planned premium upgradeplanned premium upgrade in the works. But it is open source, the project hosted on Github, and so you can run your own server as well.
In terms of features, it meets these requirements from OP:
- tagging on notes
- Markdown editor for notes
- cross-platform apps (specifically OSX and Android already avaialbleavailable)
- (were there more?)
Well worth a look, since it looks like it could meet OP's needs nicely.