No pre-made org software has ever felt comfortable enough for me, so I roll my own.
I have a series of text files organized how I like. I added syntax highlighting in TextMate. I also wrote Ruby scripts that automate any parts that would be tedious if done manually. My calendar is just a glorified text file, specially formatted for ease-of-use.
I also wrote my own TextMate bundle that turns TextMate into a wiki, which is my exobrain.
Finally, whatever you end up doing, I would recommend doing something similar to my "jot" script. Basically, whenever I have an idea or come across something I want to address later, I hit F10, a dialog appears, I type my thought into the text box and hit enter, and then the message is saved in a file called jot.txt. At the end of the day I clean out my jot.txt. This allows me to capture ideas as they come to me without breaking my momentum of what I'm currently working on. You can find that script here: http://techiferous.com/2009/12/streamlining-your-workflow-wi...