Usability could be improved a bit. For example, alloc_timeralloc_timer() (note, name is deceptive as no actual allocation takes place) could be put inside of the set_timerset_timer() function. Let your framework worry about finding a free timer in the pool, or returning an error code. A separate function for allocating the timer would be more useful if you weren't using a pool and if it was important for a user to control when memory allocations occur.
I don't like how the callback method controls whether the timer is freed. I could see lots of potential timer 'leaks'. I think if you added a repeating timer type, most of the cases where you wouldn't want to free your timer could then be taken care of by your framework. If you really need a handle to a timer that you could guarantee would be available when you need it, I think extending or overloading alloc_timeralloc_timer() (and/or set_timerset_timer()) would be a better place. That way, the decision to take it off and put it back on the free_timersfree_timers list is in the same line of code.
In clock_tickclock_tick(), you're removing aan element off the active_timersactive_timers list while you iterate over it. In your case it looks like it'll work but that's usually an unsafe thing to do, I'd double check that.
