IMHO, the windows version of Dynomation had a couple of important improvements over the DOS version, and the new version 5 is a nice improvement in several ways. It offers improved cam input with ramp rate and rocker ratio alterations. The older versions seemed to like more lift and duration than worked in reality, and the version 5 seems to address this a bit. The modeling looks to be closer to real world than before (compared to actual dyno results from past engines built), with good graphing that lets you see trends better than the old DOS version.
Larry Meaux's inexpensive PipeMax program is very good at optomizing intake and exhaust details - especially if you already have good dyno data. Basicly it does all the length/diameter/taper calculations I used to do the hard way.
PipeMax36xp2
Patrik Hale/RSR offers Engine Pro that is also a decent, relatively inexpensive program -
Advanced Engine Simulation Software for Racing & Motorsports
Blair's newest software is very good from what I have seen, but I have only worked with the early versions -
Prof Blair & Associates Home Page
I have never seen the simulation stuff from Lotus Engineering, but reports indicate it is very good, but expensive.
If you have experience with the DOS version of Dynomation, you understand that there are issues with most any engine simulation if you incorrectly model aspects of an engine, or if you expect too much from them. They are good to help optimize certain aspects of an engine that you have had on a dyno or track, or if you are looking to see trends on an engine design that you are just starting to work with from scratch.
I use simulations mostly for help with older V8 engine designs, and when working on optomizing intake, exhaust, cam details on motorcycle engines for road and track. Most are based on prior results from engines built in the past - this improves accuracy, but is usless when working outside of the software's abilities or "experience" range. Some of the simulations are good for seeing trends, but don't put too much stock in the final numbers they show.
For those who spend a lot of time working on similar engines/packages on an engine dyno, I doubt that simulation software is worthwile, but for the hobbiest, I feel that it can help educate and reduce expenses, but this is just my .02 (not corrected for the devaluing Dollar, nor inflation).
At this point, I dream of owning or having access to a good CFD software package and rapid prototyping equipment that wouldn't cost me my left..... leg.
I figure we are about 5-10 years from this.
I hope this helps,
DVS