I was just about to mention this. For me, on squats and deads muscular failure often sets in well ahead of neurological fatigue, depending on if I'm using wave loading, pyramids, or straight sets. If I'm doing straight 5x5 for example, no way in hell can I superset. On the other hand, supersetting a pyramid has been fine in the past. Also, now that I've tried wave loading with supersets, I absolutely love it and will probably incorporate it into my training.
All in all, I think you can just about ALWAYS superset upper body exercises. I wouldn't superset the toughest exercises though - for me, that would be pull-ups and push presses, for example. But stuff like bench press and curls - why the hell not?
To summarise, I would favor supersets for upper body most times, but only sometimes for the lower body. However, you have to try this for yourself and see if it works or not. I also fully believe that as the amount of weight I move goes up, I will need bigger rest periods so my CNS recovers between sets, and then I might rule out supersets. But thus far, they haven't hampered my progress.
(This is all just my personal opinion from a limited amount of observations, but hopefully this'll help)