Of the most-cited 20 papers in CS (from citeseer), the affiliation of the first author of all but four is with academia:

Academia --------

1) Maximum likelihood from incomplete data via the EM algorithm, 1977. Dempster, Harvard.

2) Communicating sequential processes, 1978. Hoare, Oxford at time of publication.

4) Chord: A scalable peer-to-peer lookup service for internet applications, 2001. Stocia, Berkeley.

5) Distinctive Image Features from Scale-Invariant Keypoints, 2004. Lowe, UBC.

6) Induction of Decision Trees, 1986. Quinlan, New South Wales Institute of Technology.

7) Reinforcement Learning: An introduction, 1998. Sutton, UAlberta.

9) Graph-based Algorithms for Boolean Function Manipulation, 1986. Bryant, CalTech.

10) Scheduling Algorithms for Multiprogramming in a Hard-Real-Time Environment, 1973. Liu, MIT.

11) The anatomy of a large-scale hypertextual web search engine, 1998. Brin, Stanford.

12) A method for obtaining digital signatures and public-key cryptosystems, 1978. Rivest, MIT.

14) A scalable content-addressable network, 2001. Ratnasamy, Berkeley.

15) New directions in cryptography, 1976. Diffie, Stanford.

16) Eigenfaces for recognition, 1991. Turk, MIT.

17) Authoritative sources in a hyperlinked environment, 1999. Kleinberg, Cornell.

18) Indexing by latent semantic analysis, 1990. Deerwester, UChicago.

20) Handbook of Applied Cryptography, 1996. Menezes, UWaterloo.

Industry --------

3) A tutorial on hidden Markov models and selected applications in speech recognition, 1989. LR Rabiner, Bell Labs.

8) Optimization by simulation annealing, 1983. Kirkpatrick, IBM.

13) Snakes — active contour models, 1987. Kass, Schlumberger Palo Alto Research.

19) Fast algorithms for mining association rules, 1994. Agrawal, IBM.