How are you going to offload this counting to a PC? Through the serial port?
Anyway, for the 2 x 6000 counts you could use external interrupts, and pin changes on the slower ones. The trouble with pin change interrupts is you only get one interrupt per port, so you have to spend time working out which pin changed (out of the 8 possible).
However I would still be tempted to use the internal timers for at least the high-speed events. You could then count how many happen in (say) a second, and upload the counts, plus the counts from the other interrupts, to the PC once a second.
(edit) Ninja'd by el_supremo ... yeah, what he said.