Since now, when I am analyzing a binary, I'm using a "pen and paper" method to locate the different location of the function, the different type of obfuscations, and all my discoveries. It is quite inefficient and do not scale at all when I try to analyze big binaries.
I know that IDAPro is having a data-base to store comments and a memory zone, but, in case we do not want to use IDAPro, what techniques or (free) tools are you using to collect your notes and to display it properly ?
radare2 does support projects. They are not as sophisticated as IDAs .idb format, but they do the trick if saving patches and comments is all that you want. (Just make sure to build it from git)
Taken from the Radare2 Github README:
Webserver
radare2 comes with an embedded webserver that serves a pure html/js interface that sends ajax queries to the core and aims to implement an usable UI for phones, tablets and desktops.
$ r2 -c=H /bin/ls
You know, there was talks before about coming up with some kind of standard to share RE notes on woodman forums, that would be nice. But I usually just try and stay as neat as possible using notepad, and for collaborative work, I use Google Docs as well. Lately I have taken up using Evernote for collaborative work too, only because using Google docs requires me to use the web interface for their document format.
When I work on a really complex project where I need to make a lot of structured notes, I often use tiddly wiki. The nice thing about it is that you can easily backup the wiki since it simply writes to its own html file.
And of course Google Docs, which is especially useful if you're working collaboratively.
If you can't/don't want to use IDAPro, perhaps you can/may want to use another automation tool. ScratchABit is an open-source, interactive, direct-manipulation(*) disassembler which stores all the information in simple text files, not a proprietary binary database. From these text files, the information can be easily extracted with simple scripts, or they can be stored in version control system to allow collaborative work, etc.
Full disclosure: I'm the author of ScratchABit and it is work-in-progress project.
(*) Direct manipulation means that you press a command key and immediately get a reaction, you don't need to type long commands with manually specified addresses and press Enter.
Currently I'm using TreeDBNotes, they have a free and pro version available. I haven't compared it to any of the methods mentioned in other answers, but find it quite useful for keeping track of my project notes/data.
