It sounds like you have a lot of experience in this area. I admit I've only really touched on it before on projects I've worked on. Do you know if there's any good books or online guides on this subject, as I find it quite hard to devise these systems myself?
You may want to go through fravia.org archives. It's old, but basic protection principles don't change that quickly (or, looking at it from the other end, rudimentary cracking techniques are the same as well).