CTools plugins system

When we are writing our own module we, as good developers, should allow other people extend/modify some parts of it. Yes we are talking about defining our own module's hooks. But what we can do if we need to "extend" our module in several places but we should be sured that other module that implements one hook should also implement another one? What we should do if we have a lot of such cases and we should take care about consistency of implementations of other modules? Also sometimes we would like user to decide what implementation to run (so we want some kind of administration page where we select what extention to be active).