Program Obfuscation

Program-Transformation.Org: The Program Transformation Wiki

Obfuscation is a ProgramTransformation that makes a program harder to understand by renaming variables, inserting dead code, etc. Obfuscation is done to hide the business rules embedded in software by making it harder to reverse engineer the program.

Gregory Wroblewski's work seems to have a good summary of work on the obfuscation of binary programs. His web page is http://www.mysz.org/publications.html.
Christian Collberg is a pioneer in obfuscation. See his page titled Robust Obfuscation.
There are many obfuscators for Java. See for example yGuard.
PreEmptive Solutions has a product called Dotfuscator for CLI/MSIL/.NET, a light version of which will be distributed with the next release of Microsoft® Visual Studio® .NET.