edit: I have a question on this actually. How do you guys feel about on rare occasions running into pockets of super mutants?
Well, if you've done Black Mountain - Neil specifically states that super mutants periodically show up at Black Mountain.
The only places with hostile SMs though are Black Mountain (which needs more spawns, especially on the NE slope downward) and the very NW corner of the map out past a ranger station. Up there could probably use a few more solo spawn points, but it would have to be mixed in with the ghouls. I'm ignoring the ones you run across in Novac, those are solo crazies and it wouldn't make sense to have more there.
Possibly along the south edge of the map you might be able to pack a few in. Maybe down towards the SE corner too.
I envision solo super mutants, maybe a trio, but keeping a low profile, so a very small footprint. Possibly a stealthed nightkin here and there. There's just not that much room for them with the various bandits. Definitely keeping to the edges of the map, or crammed into very small locations on their way to either Jacobstown or Black Mountain.
Not sure I'd put any in the hills up near Jacobstown, at least nothing within a few cells of Jacobstown proper. Maybe 1-2 solo crazies along the road up from NE Vegas.
I can't see them being too close to Vegas either. NCR would drive them out, or they would get into constant fights with the fiends on the west side.
They're just not a powerful force in New Vegas. Bit part players, stuffed into the edges of the map is their role.