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(Co)chain complexes, abelian Categories, (pre)sheaves, (co)homology in various (possibly highly generalized) settings, spectra, derived functors, resolutions, spectral sequences, homotopy categories. Chain complexes in an abelian category form the heart of homological algebra.
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Nondegenerate pairings versus perfect pairings for finitely generated projective modules
No: for $R=\mathbb{Z}$ and even for $M,N$ both free (i.e. free Abelian groups), non-degenerate doesn't imply perfect. (You get finite index sublattices, so torsion quotients, unlike the case of vector …