Plenty of information out there regarding what to look for, main things are service history, belts etc.
The only major difference between the two will be capacity but this depends on model, the original '99 996 was pretty much the same as a 916, but there are various models across both ranges so you need to decide which you are looking at, most will have been modified by now I'm sure, termi's, shoch, carbon, bling etc anyway.
I've ridden both and owned a 996 and didn't think there was that much between them.