DES uses 6 by 4 s-boxes. More recent ciphers such as Blowfish and CAST-128 use 8 by 32.
There has been a great deal of research into the design of good s-boxes. One excellent paper is: S. Mister and C. Adams, "Practical S-Box Design," Workshop on Selected Areas in Cryptography (SAC '96) Workshop Record, Queens University, 1996, pp. 61--76. It is online as PDF at http://adonis.ee.queensu.ca:8000/sac/sac96/papers
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