I wouldn't rely on the cheap or free one's to be real accurate but they can be used as an indicator and guideline. The expensive programs are fairly accurate but again, you don't really know until it's on the dyno and you are getting "real" numbers.
Check on the CompCams web site, somebody said they have a program you can download...theres some others. You can buy the cheap ones for $40 or so. Personally I would rely on a professional engine builder or go with a know combination, or buy a crate engine that's already been dyno'd so you know what you have.