A few years back Byron Jacobs, John Emms, and Jacob Aagaard co-wrote a book, Chess Software Users Guide. It did a great job of explaining just what you're asking about. John Nunn's Secrets of Practical Chess includes an excellent chapter on the subject, as does Improve Your Chess At Any Age by Andy Hortillosa.
How to use computer to improve
Can anyone point me to some online guides, articles, or videos on how to best use a chess program to improve one's game? I've got access to Chessmaster GE, Rybka 4, and this site. I have found them useful to analyze my games to see where I made serious errors, but I imagine that I could get much more use out of them. One of GM Dzindzichashvilli's videos (http://www.chess.com/video/player/no-exceptions) mentions using Rybka to train for playing positionally, but I'm not sure exactly how I'd do that.
Try to look up chess hero. In my opinion it is the best tool which allows you to use Rybka as a chess teacher.

These 3 links should give you all that you need:
http://www.chesscafe.com/text/heisman25.pdf
http://www.chesscafe.com/text/mig02.pdf
http://www.chesscafe.com/text/lopez05.pdf
Can anyone point me to some online guides, articles, or videos on how to best use a chess program to improve one's game? I've got access to Chessmaster GE, Rybka 4, and this site. I have found them useful to analyze my games to see where I made serious errors, but I imagine that I could get much more use out of them. One of GM Dzindzichashvilli's videos (http://www.chess.com/video/player/no-exceptions) mentions using Rybka to train for playing positionally, but I'm not sure exactly how I'd do that.