There are a number of papers that I have affection for. Those which I don't see listed:

"On the group completion of a simplicial monoid." Before I read this paper I never really understood the appearance of the plus-construction. This essentially proves the +=Q theorem. (A little harder to find: Appendix Q in Friedlander-Mazur's "Filtrations on the homology of algebraic varieties.")

"On the formal group laws of unoriented and complex cobordism theory." A very influential paper, along the likes that Mark Grant mentioned, and one which we've been trying to unravel the consequences of ever since. (Bull. Amer. Math. Soc. 75 1969, 1293–1298.)

"The Adams conjecture." Quillen's proof of the Adams conjecture by making use of a Brauer lift is short but wonderful. (Topology 10 1971 67–80.)