Two papers I would include are:
D. Kozen, "Indexing of subrecursive classes", STOC, 1978.
R. Ladner, "On the Structure of Polynomial Time Reducibility", JACM, 1975.
Hajek, P. Arithmetical hierarchy and complexity of computation. Theoret. Comp. Sci. 8 (2): 227-237, 1979. Started the study of the complexities of index sets (where their "complexities" often lie somewhere in the arithmetical hierarchy; see this answer to another question.)
On the study of polynomial-time degrees (buzzword="polynomial-time degree theory", for the sake of future searches) I'd say these papers are of interest (several of them are based on Ladner's technique):
Probably a forward and backwards reference search will find several more papers in the same area (though it's not that big an area!).