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.)