I guess it depends on what aspects of the engine you want to simulate and for what purpose. For performance prediction some colleagues have had reasonably good results (correlating with real engine data for full load torque) with the Lotus Engineering freeware found at
I have used both programs and have found that I really like the Engine Analyzer Pro 3.3 from Performance Trands the best. It is easier to use and gives me results that are very close to actual dyno tests that I have done and had access to. Many different inputs that you can test. I have actually done beta testing for Kevin at Performance Trends so yes I am a little biased. Just always remember garbage in and garbage out rule when working with computer programs. EAP 3.3 let's the user input actual cam files that have been created by profiling an actual cam. You can also input the actual flow from cylinder head tests that you have done. The repeatability is very good. Best is the fact that the results I get in EAP 3.3 come so close to actual dyno tests that I have done. This allows me to do a lot of engine testing and building without spending the dollars. Keep in mind, and all the pro's will verify, the best dyno or simulation program is the track.