If you want a specific thing frequently, make a convenient place for that specific thing, or some small number of specific things.The only problems I see with this arrangement is that you still can't just reach for something and put your hand right on it. You have to fish around thru the writing tools to get what you want.
If you have tons of writing implements but can divide them into a few useful categories (black pen, blue pen, pencil, highlighters, permanent markers, marker board markers), you have 2 choices: 1) sort them into 6 appropriately-sized containers, or 2) get rid of all the excess, or at least relegate them to longer-term storage and replace as necessary. I personally keep 1 or 2 of each type I often use handy on my desktop, and store all the backups in one container in a desk drawer.
(The Container Store sells some custom drawer dividers that are awesome for this kind of thing -- completely customizable. Whenever you store lots of small things in big drawers, these dividers RULE.)
If you have 100 completely different writing tools and need to put your hand instantly on THE EXACT one you want, you need a pen-organizing system that is beyond the scope of any organizing book I've seen, and I bet that David Allen doesn't have an instant solution for you either. But I'm sure you can figure out something that will work well enough for you.