I don't know much about the NES.
It was before my time after all. Talk to me about PS1 and PS2 subsets.
Square RPGs
That's one that I'm working on.
For NES subsets, as a boxed collector, I started collecting subsets with similar boxes.
Capcom- There are several different box styles, the Section Z.Mega Man 1 type with the crossing lasers and the Mega Man 4 "purple border" type. I had them separated at first but now all Capcoms are alphabetical. They are similar enough where they look good mixed
Tecmo-most of my Tecmo games have that red bar across the bottom that extends to the spine. This makes the games really stand out when grouped together.
Konami Silver Box games-Maybe my favorite NES box style apart from NES black box games. They look great grouped together as carts or boxes.
NES Black Box The most expensive subset if you are going for CIB, not really too bad if you are just going for cart only except for Donkey Kong Jr Math.