3x5 cards and binder clips have been a part of my "portable" kit of idea capturing and organization--they're more durable than Post-It notes. Always write on the fronts of the cards only so that you can tape or glue them into my other more permanent kit data storage, the composition book. 3x5 cards and composition books are ubiquitous--you'll almost never be able to buy them. These are only going to be for your direct personal use--for collaboration, you'll need to escalate to something else.
Group Situations (In Person)
Besides Post-Its, 3M makes giant "Easel pads"-- and these are far superior than trying to use a whiteboard for group brainstorming. When you're finished with your room and meeting, you can take them with you to summarize into some other system--maybe something as simple as a digital camera and a tripod to digitize them.
Group Situations (Virtual)
This is where things get tricky. I have never seen a digital whiteboard system that effectively captures the spirit of interaction between people in the same room. (Plus, they're expensive.) Not everyone can be on the same platform and owning the same software or hardware. It really depends on how interactive your communications are. If everyone's spread out across 5 wildly different time-zones, you'll need something like e-mail or wiki to keep interactions asynchronous. A collaborative blog can be useful. If you're lucky and everyone is within the same realm of time, Internet Relay Chat or some other group-chatting system (as long as you can archive it) is good. In the end, with a virtual situation, you need to pick and solidly decide on which particular protocols or applications you're going to use or your ability to keep attention on what the group is doing will be hopelessly fragmented.
K.I.S.S. and K.I.C.S.
Everyone's heard of K.I.S.S, I'm going to add K.I.C.S. to the mix: Keep It Consistent, Stupid. There's a theme here: do the simplest thing that could possibly work and stick to it until it doesn't work. It is far too easy to fall into "yak shaving" trying to find the best tool for the job by trying out all of the New! and Exciting! and Technologically-Sweet! tools the come around the bend. Do that in your spare time (like you have any). Everyone has e-mail and everyone has a web browser. Paper requires no software, batteries or training. Well, maybe not so much on the training. :)
Digital Paper is an Abomination
3x5 cards or composition books... what about this digital stuff, it sounds great-- a special pen, special paper, special software. It is not cheap however, the cost of paper being orders of magnitude more expensive than ordinary paper and in addition, you must use a special pen to write with (what happens when a friend annotates your paper with their favorite Zebra pen? Now you'll have to scan your paper again or trace their handwriting with your special pen--this is "simpler?"). Let's not get into the can of worms involved with privacy--since all digital paper on the market today seems to be systems to uniquely assign ownership to tiny areas of virtual paper-space. Stay away from digital paper systems, they're not KISS/KICS.
On Organizing Ideas
Capture. Review. Summarize. When capturing, date-stamp your notes with a brief title on why you were writing them. Nothing is more frustrating than seeing your own handwriting describing an idea and not understanding why you were writing about it. Write down the questions and goals or missions you're considering. You may not have any thoughts on them today, but days after you have captured your questions or ideas, review them, because you're likely to have new view points on them. Repeat this process until you can summarize the intents of your idea or inventions--now is the time to bring it to others for out-of-singular-mind brainstorming. [Or not, some ideas are just inherently bad. Keep them to yourself. ;) ] The beauty of using paper is it will never distract you with red squiggly lines of spell checking or frustrate you with ham-fisted mouse-drawing limitations because you don't own a graphics tablet. Just draw it. It doesn't have to "look good" until you understand it intimately and you're ready to share it with others. Sharing comes after understanding. Keeping things dated and sequenced properly helps you review and discard the old notes. Don't be afraid to re-write them again forward in your notebooks if it helps you consolidate the amount of paper you need to manage (notebook defragging).
Overcoming the Limitations
No one sits down to write the Lionel Gelber Prize-winning tome in one perfect marthon session, so you shouldn't expect your programming notes to be instantly perfect the first time you write them on paper or share them over e-mail. The more hours you exercise your mind upon the paper, the better you'll become. They say that for writers to become better writers they must write. For a programmer to become a better organizer you must, organize. For me, all too often, it's easier to do it on paper than to do it on a machine. Management of ideas to me is all about the distillation and summary of those ideas. You can't manage something you don't understand. Don't worry about wasting paper--because turning back the pages you've written before is nothing other than paper's implementation of ^Z.