I guess the most common things I do beyond the NEC are these.
1)Supports: raceways, cables, enclosures etc. beyond the code minimums and then some.
2)Wire Size: usually one or more sizes up from minimum.
3)Raceway Size: again one or more sizes up from minimum.
4)Identification: Mark panel and circuit designations on J-Box covers, utilization equipment etc.
I will be thinking of this question some more, it is a good one.