A few of my favorites, chosen from computer science and from physics:

D. E. Knuth, "An empirical study of FORTRAN programs," Software: Practice and Experience, vol. 1, no. 2, pp. 105-133, 1971. http://dx.doi.org/10.1002/spe.4380010203

  A choice quote: "A first idea for obtaining 'typical' programs was to go to
  Stanford's Computation Center and rummage in the waste baskets and the recycling
  bins.  This gave results but showed immediately what should have been obvious:
  waste-baskets usually receive undebugged programs."

D. E. Knuth, "The errors of TeX," Software: Practice and Experience, vol. 19, no. 7, pp. 607-685, 1989. http://dx.doi.org/10.1002/spe.4380190702

  Knuth recounts and analyzes the process of developing the TeX computer typesetting
  system.

A. Einstein, "Zur elektrodynamik bewegter körper," Annalen der Physik, vol. 322, no. 10, pp. 891-921, 1905. http://dx.doi.org/10.1002/andp.19053221004

  Einstein's seminal paper "On the Electrodynamics of Moving Bodies" that proposed
  the theory of special relativity.  A good English translation is available online
  at http://www.fourmilab.ch/etexts/einstein/specrel/specrel.pdf