An interesting read can be found on the following article by Randy Brown. Homemade KJV Looseleaf Bibles are a great study aid, and like the article Randy links to suggests, having a few chapters or books of the bible in a loose leaf binder makes for a great way to study out the scriptures. As you comment on the scriptures and write your notes, take a few minutes to write them down in a word processor as well. Before you know it, you’ll have collected a wealth of information on the bible as your studies grow and mature.
I am a big fan of using the computer for my notes, and I typically use Olivetree’s Bible Reader on my iPhone and sync the notes with the Evernote server. I can then go online to my Evernote account and cut and paste my notes I’ve collected into a personal wiki. This wiki then becomes my own personal commentary which I can then feed off of for sermon material, as well as for posting into forums!
A good Desktop wiki like product for the Microsoft users out there is WikidPad which is an Open Source Wiki which is great for note taking and really helps storing all of those great nuggets you’ll collect over time. For brainstorming, I always recommend using Freemind which is an Open Source mind mapping application available for Windows, Mac and Linux. I encourage you to check it out!