I would always opt for the 48V system, unless you are trying for a minimal battery pack. You never have to use all the speed/acceleration you have available, but if you get the 36V system you may end up with less speed/acceleration then you desire under some conditions. As far as range, you will use the same Watt Hours on either system if you ride at the same speeds.
I just read Sunder's post after typing the above, and I agree, except I always think in terms of a mid drive now, such as a BBS02, where you can select the gearing that lets your motor run near its sweet spot at any speed.