I've found Zotero to be very convenient for managing notes alongside where they matter for me at least, which is alongside documents and images. You can also link related entries and add tags. The notes are very basic, so probably lack many useful features found in Evernotes, but they're good enough for my purposes. Related to Evernotes financials though, who can say where it's going to be as a product in the next couple years? The real thing that I like most about Zotero is that it is open source, has a local data store with a simple sqlite database, and is developed by a non-profit. If your notes are ephemeral, there are miriad other options. But if you want to keep them long term and preserve their connections to other content, I think you have to be able to easily parse and port them yourself.