After seeing this video of Monotrail Tech Talk, I've settled to a "function" organization.
Basically he divides systems in four main categories :
1) The MonoSynth
2) The Sonic Exploration Lab
3) The Performance System
4) The Dedicated Tool
It helped me a lot to think about my systems this way.
Within a case, I follow the signal flow from left to right, with sequencers in the middle.