It's generally established that Vault 87 was a location in which the Enclave performed tests with different strains of the FEV, which it is believed led to the development of local Super Mutants, who apparently continue to create Super Mutants using the FEV.
I believe Sid is a super-mutant. Or more accurately, a super-human. This is for one basic reason: Sid is exceptionally tough, with a base health of 70 (in comparison, most NPCs have base healths of 10-20; Talon Company have a base of about 20-35). Sid also has a level multiplier; he can potentially have up to 160 health, which is many times higher than normal humans, though not quite Super Mutant level. While he is not exceptionally strong, none could argue the benefit of a super-tough soldier able to take much more damage than an average man.
The question is, then, how was Sid created, and by whom? Has Sid been locked up in that holding cell for 200 years like Fawkes? If so, this would add to the probability of him being a super-human. And if he hasn't been there for 200 years, and was placed their by the Super Mutants who occupy Vault 87, that means that super-men like him are created today.
Another question is how he was created. More than likely he is a rare, maybe unique, creation of the regular Forced Evolutionary Virus (perhaps the only truely successful subject ever made?). Sid is, however, hostile to everybody, including Super Mutants (he will attack and kill the Centaur also located in a nearby holding cell). This hostility could be due to two reasons: After 200 years of incarceration he has become insane and will attack anything on site; or the unique transformation which led to his increased strength without any of the physical changes inherent in regular super-mutants did not include turning him into an idiot, and thus he never "joined" the super-mutants -- instead he was locked up, perhaps kept alive because the super-mutants admired his exceptional strength.
Whatever the case, it makes for an interesting question and plot. If Sid was created post-war by the Super Mutants, could there be more who escaped? Could Vault 87 have been initially successful in its experimentations, with the process that creates modern super-mutants due to something else? Perhaps although they created the perfect soldier, he became unusually aggressive; further changes resulted in the modern super mutant; still highly aggressive, with child-like intelligence, but capable of forming co-operative communities.