In Steven Wolfram's blog entries, he discusses using mathematica to discover algorithms. I have tried several different google searches for papers on such topics, and have found none. I suspect this is a case where I'm not using the proper search terms. I could imagine some sort of genetic algorithm based approach that takes a genome and turns that into an algorithm, but I would be curious what specifically he is discussing.
The example I'm familiar with is the claim that some of the formulae used internally by Mathematica's functions were derived using Mathematica itself.
We can of course presume that the formulae themselves and how exactly they were generated is a trade secret. ;)