Sick of storing all your notes on someone else's server? Magpie is a simple, web-based notes app you can host yourself that features notebooks, notes and PDF scraping.
Once you set up Magpie on your server (or on GitHub or BitBucket), you can create notebooks to store and organise your notes. You can also set it up to email notes and scrape through PDFs to make them searchable. It's certainly not as advanced as Evernote, but if you'd prefer to keep all your notes on your own computer (or wherever else), Magpie's a pretty simple way to do it.