SMWS (Mitsuo Oiso of Yokohama, Japan) sent me two letters describing some interesting algorithms he uses for solving ciphers with a computer. I found his Quagmire IV algorithm to be very effective. With his permission I've scanned his letters and posted links to them below. Update: There is now a third letter with his Digrafid hill-climbing algorithm (see below).
Letter 1 (algorithms for swagman, hill-climbing for simple substitution, playfair, Phillips)
Letter 2 (More on hill-climbing, Quagmire IV algorithm)
In letter 2, the algorithm of mine that he refers to is PH hill-climbing, see that topic in the algorithms section.
Letter 3 (Digrafid hill-climbing algorithm)
I have not tried his Digrafid algorithm yet, but judging by SMWS's Quagmire IV algorithm, it should work well.