I feel you man, I'm also a long time Evernote user who got sick of the web app on Ubuntu (especially with the recent redesign!).
I tried some other stuff but eventually settled on Geeknote, which is strictly for text notes. You can bring them up really quickly and you can even browse your notes as a directory tree in vim with this plugin! If you aren't a big fan of the command line I fear the web app is probably your best choice though.
Thanks, I've already used the Todo.txt method, and while it works great on the desktop (The CLI tool is quite good, I even rewrote it in Python) I find the Android app to be lacking, even slightly expensive.
I really wish I could get Geeknote to work on Linux Mint 13, it seems to be the perfect solution. It's a CLI tool for Evernote, lets you create and retrieve notes as plain text files. Exactly what I'm looking for!
I agree that plain text files usually suffice. Though they become complicated once you sync it between machines.
One useful tool may be a static site generator like [hugo](static site generator), this could create nice views based on tags and also embed other files.
Since it wasn't mentioned there are also cli tools for note keeping software like for evernote there is geeknote.