So, I found about this great tool for organizing notes while you do the penetration testing.
It’s basically a simple note-taking app called Dradis specifically designed to be used in penetration testing purposes. It’s open source, written in Ruby and runs straight in your browser.
Everything you write down for a project will be password encrypted and stored in a SQLite database.
It does not have text formatting option, so you can’t really rely on your notes to look pretty, but it has an option of importing data from some of the most known intelligence gathering applications.
Although I was impressed that there is a tool specifically designed for using for penetration testing purposes, it’s not something I will be using. Although I’m actively searching for a good Evernote alternative (I do not feel comfortable storing my notes on their server and I’m not comfortable that my notes are not encrypted on my hard drive), I got kinda used to using it, so I will be using Evernote at least for a while, while I’m still trying to find some good alternative that has my privacy as their main goal, but can also sync my notes on both of my systems (Windows 8.1 and elementary OS of course).