Be interesting to peer inside each of our own 'systems' that produce a site.... I am pleased to share mine:
I am full of ideas - so I need a robust depository to collect and organize these which continue to keep compounding over time...
I prefer to work with paper so I can walk about, get the oxygen pumping and 'reflect' which I think is an often neglected and critical part of the success equation for generating content for example.
I make sure I carry a pen everywhere as one tiny idea or insight can change everything in this business so I make damn sure I write it down, and categorize it immediately. The moment things don't get categorized mess creeps in and the system starts to crumble... or frustration starts killing creativity.
I have a how to pile in front of me all the time of print outs of favorite articles which I skim read - 24 hours/ 7 days then monthly recapping. I have another pile for jotching, doodling and sketching random thoughts, keywords which I call a tickler file - for flicking. I have a business dev pile for any idea which influences the structure of the company. I also have a meticulously categorized content pile for blog/ principles/ verbs and adjectives which are really inspirational for 'describing' or 'actively doing' in my niche... Then the good old intray which is low low priority - profit before bills :)
For me... ideas are stuffed into a dated/month long tickler file (if not implemented immediately)... then I check that file every month to see if that "idea" is still interesting/valid. If it is, then it gets implemented. If not, an x in upper right. Two xx's and it gets tossed. Not all "ideas" are good... :)