Is there a consolidated list somewhere of the various AVR hardware features used in the Arduino?
Basically no. The Arduino uses most of the hardware features in one for or another.
The data sheet is great in seeing what is available but the only thing I can think of they don't use is analogue comparator.
what's open for the user to use.
You can use them all.
Basically what you want to know is what will you loose if you mess about with some of these resources. For example all three timers are used for PWM as well as timer 0 doubling up for the millis functions. But you can use them if you don't mind not having that particular function.
Resource management is always a bit tricky especially if you are using libraries that do not state up front what resources they use.