After talking to Josh for a bit, we decided that we should overhaul hooks a bit before putting out 3.0. The reasons for this are mostly that the existing hook system didn't allow module developers to build hooks easily and have those hooks referenceable by other modules written by other developers.
I just finished coding up the HookManager class which holds registered hooks. Hooks can now be retrieved via the old method (accessing the Hook directly) or alternatively through the exported module which talks to the HookManager which knows about all registered hooks. I spent some time overhauling the existing Lyntin code to account for this adjustment and it's working nicely so far.
Hopefully this is the last big issue to solve before 3.0. It needs to sit and cook for a bit, though, so this will push the 3.0 release off at least a week--possibly more.