I have several, because each program omits some important information, no one program provides enough information. The one I use the most is an old dos version of Engine Analyzer v2.5 by Performance Trends. It is so useful that Im still finding new ways to use it (especially for intake manifold construction).
THe other is Racing Systems Analysis, Engine Pro v3.1 by Patric Hale. It is unusual in that the intake cam lobe dimensions, intake manifold, and head flow are input and his program recommends the other perameters. (specific for drag racing engines only) It is the only program that I know of that plots port flow versus piston and valve position. Ever wonder at what piston position and valve lift the maximum port flow occured during the intake cycle? It even provides specific cfm flow and inches of vacuum at each valve and piston position. You can dublicate the perameters on a flow bench to match the flow requirement to each valve lift position.For example for a 240 ford max piston speed during the intake stroke occures at 77.4 deg when the intake valve is open to .568 lift. Guess at what valve lift the port should be flow tested and for max cfm? It really answers many questions we all were afraid to ask.
Another program that helps the drag racer is Performance Trends - Drag Race Analyzer. It can tell you when your cam duration is too large and you killed off torque needed to pull that big 14" drag slick. Just plug in your converter stall and engine torque curve.
No one program claimes to give all the answers, but it gives an educated place to start on an odd ball racing combination like a 240 six in a 1700# street/drag roadster.