Is this for an RPG project, some proxies for a wargame, or just painting them up for fun?
This would be for a wargame. Most likely Tomorrow's War, WarEngine or one of the other Generic (not tied to a particular figure line) wargames that my club plays
The first alternate head option looks interesting. (What is the manufacturer? I can't figure out how to find the origin of the image.)
It's by Pig Iron. I've used alot of their heads in conversions, but not this particular model
If I was in a GI Joe knock-off game and I had to fight some guys with those helmets painted blue, and red or silver face plates, I'd fully accept them as being some sort of Cobra trooper and not fret over-much. After all, the look of Cobra has changed a lot over the years.
For the record, the classic viper figure that inspired the choice of the first helmet is this one

Also he's got more armor (unlike the blueshirted cobra troopers) so he'd better fit the Nova trooper look and as you say they have changed over the years and there have been dozens of Viper variants. I think I'll probably go with making them into Vipers.
The last head options, however, look awfully blocky. I assume that with that option you're not even trying for Cobra anymore, but I think part of the problem is that those heads are just too sharp and angular to fit with the armor, period.
Yeah, I just tossed them in because I liked the look, but they really don't fit the armor or the Cobra asthetic.
As for myself, I'm pondering getting an extra set of NOVA Corps troopers, putting them on 25mm round bases with some sort of techno texturing, and painting them up as generic futuristic "corporate security." For a little variety, I might do a couple of helmet/head swaps -- for instance, I could grab one of the regular troopers, give his helmet to the bare-headed NOVA Corp Hero model, then give the newly-headless trooper a head-swap from my bitz box -- possibly someone with some futuristic headgear, and turn that character into some sort of specialist (medic, etc.).
I was also thinking about perhaps taking some extra Corps troopers and turning them into zombies or mutants, for some sort of space opera sci-horror setting. For that, I'd probably need a few plastic zombies (once they're more generally available in packs), or else I could go some sort of mutant/horror route and get a tentacle pack and have some troopers mutating a la the Flood from Halo. That way, I'd have something for my IMEF troopers (and my non-mutated NOVA Corps troopers) to shoot up, since so far there aren't any Bones Cyber-Reavers, Kulathians, or other swarming space-horrors.
Sounds like a cool project. For nameless baddies, there a number of sources for cheap plastic zombies, aliens or troopers. No need to cut up nice Reaper figs to get the parts to convert them with.