Jeffrey Baumgartner of The InnovationTools weblog had a nice idea for managing the maelstrom in your head without it getting in the way of your work. Brainstorming technique - Multi-thinking - from InnovationTools
Whether you multi-task or not, you almost certainly have numerous tasks awaiting your attention at any given time. And it is inevitable that your mind occasionally turns to one task while you are working on another. A multi-tasker would be inclined to switch tasks at this point. I recommend you stick to the task at hand, but keep a notebook - or at least some paper nearby - when performing any tasks. (I recommend having a notebook with you all the time). When the mind turns from the task at hand to another task, simply note down your thoughts in the notebook. Then return to the task at hand.
While this is still an interruption to the task at hand, it is a structured way to have an interruption. Rather than letting those brainstorm thoughts distract you down a completely new path, jot them down for later reference and get back to what is in front of you.
I've been trying this idea since I read this a few weeks ago, and it seems to work. At the computer, I just open a quick note to write down the thought then bury the window. During more open time, I revisit the notes and file them away. Most are "nice to do" type ideas anyway, so they go in that folder.