Where does the prefix "super" from "supersymmetry" come from?
Super- means "situated over, above, higher than, or (less commonly) upon another".
The earliest usages the OED gives for supersymmetry—"Symmetry of a more general type or of a higher order; (Physics) a very general type of mathematical symmetry proposed as relating fermions and bosons"—in the physics sense are:
1958 Progr. Theoret. Physics 19 639 If there is the super symmetry between $Λ$ and $Σ$ when $gK^2/ℏc = e^2/ℏc = 0$, $Λ$ and $Σ$ must have the same intrinsic parity.
1961 S. L. Glashow & M. Gell-Mann in Ann. Physics 15 297 One of them might play a role in the physics of the strong interactions if there is an underlying super-symmetry, transcending charge independence, that is badly broken.
1966 Ann. Physics 38 554 The spectrum happens to coincide with that contained in the (6*, 6)–(6, 6*) representation of the recently proposed U6 × U6 supersymmetry.
1974 A. Salam & J. Strathdee in Physics Lett. B. 51 353/1 These authors [sc. J. Weiss and B. Zumino, 1974]..designate this Fermi-Bose symmetry by the expression ‘super-gauge’. Since the word ‘gauge’ has come to be more commonly associated with ‘gauges of the second kind’ or local symmetries, it is confusing to use super-gauge to describe what is indeed a global symmetry of fermions and bosons. We suggest therefore that the expression ‘super-symmetry’ might be more appropriate.
1975 S. Ferrara & B. Zumino in Nucl. Physics B. 87 207 Supersymmetry transformations form an extended Lie algebra.
1977 Physics Today Apr. 49/3 As far as I know, the only natural way to keep a scalar boson massless is to have a ‘supersymmetry’,..which puts scalar fields in the same multiplet as massless fermion fields.
2001 N.Y. Mag. 14 May 93/1 Paintings whose images draw on the ‘supersymmetry’ physics theory that every particle of matter possesses a ‘shadow’ particle.
2005 L. Randall Warped Passages xvii. 347 The idea was to communicate supersymmetry breaking not through the graviton, but instead through gauginos, the supersymmetric partners of the gauge bosons.
The question does not seem to be sharply formulated, so the answer will be vague: "super" comes from the way semantic evolves. Words have antonyms, usually conceived as negations, but negation can have different modalities, so instead of a pair, language usually has more terms. This idea has been developed in the semiotic square proposed by Greimas. So we have e.g. 'natural' and 'unnatural' but also 'artificial' and more over 'supernatural'. In science: symmetry and asymmentry and anti-symmetry. I doubt that 'supersymmetric' has any mental relationship with 'supernatural', but one has to know who first started using the word (and here we might recall the details behind the famous 'god particle').