Basic tools can be very traditional: The notebook and file cards. I find 3" x 5” cards ideal for tucking in a pocket or my purse (yep, I’m a girl) to make notes as they strike—just like that first idea—in the grocery store, at the movies, talking to Aunt Susie, or wherever the moment hits.
I use the notebook while waiting at the doctor’s office, waiting for a friend to show up at the café, dining out, etc. to make scene notes.
For my novel Felix Ravenna I had to populate a palace, a city and two important political centers. I used Freemind to list the characters, place them in the appropriate geographical setting, and draw arrows (different colors) to show alignments and antagonisms. If you work with visual cues this is a great tool.
I printed out the results and tacked them up on the storyboard.
For making comments while you are out doing research an audio recorder is great for on-the-spot ideas. I use a voice recorder attachment for my iPod. I just slip it in a pocket and talk as needed. This also works to capture interviews with experts as you do your research. Later, you can transcribe these notes and then place them in the appropriate file on your computer or in file folders.
If you plan on telephone interviews you may want a phone recorder as well.
The technical suggestions are useful but not necessary. For centuries, people wrote without computers, without voice recording technology or software programs.
If you love sitting in front of your computer, there are software programs that make “note cards” which you can rearrange in the program.
I am a visual and tactile person. Somehow handling my 3x5 cards, pinning them up, and rearranging them as needed helps solidify the story for me. That’s just me and how I work. The important part of this implementation step toward producing a marketable, professional story is having a place to store your information. The bits of information will grow exponentially as you do your research and start expanding your characters.