Sounds like you would be pretty happy with Android if you ask me!
The Android platform isn't mature enough right now. I'll be in the market in about a year with HTC's then offering. It'll be about the time my iPhone contract ends.
We used them a lot last year. Off the top of my head - ALICE (some super-powerful physics app), Datagraph, and a CAD application in our Engineering class.
ALICE - couldn't find anything about it on Google. Having used an educational programming language intro software called ALICE, used by CMU, I think that may be what you're talking about? That was definitely supported on all 3 platforms, though. Please do let me know what app you are talking about, otherwise.
Datagraph - seems like a relatively small add-on written for Excel and statistical packages. In fact, it's cost-point of $99 suggests that it's not a major commercial or educational software. Of course, I have no knowledge of what the program does or how it works, but I would still wager that there are Windows alternatives available.
CAD app - I've never done CAD but I know AutoCAD is some pretty serious software and as far as I am aware it's only available for Windows (or running it on Mac through Windows). So...
Terminal, the native app similar to 'run', is used ALOT in our AP Computer Science course. I'm not in it but they do some pretty heavy coding in that class, i think. In our science/math based school, we only have Macs. It's a top ranked school that offers plenty of engineering/computer courses taught by actual engineers so obviously they are doing something right.
Terminal is not similar to "run", run is a simple command that attempts to execute the file you have entered in the search path. Terminal is similar to the Windows Command Line--both are shells into the operating system. If you want to emulate the UNIX command line behavior, you can download Cygwin for Windows and get all that.
I don't know what you mean by "pretty heavy coding" but if we're talking industry then I can tell you for a fact that most real software is written on Windows machines (or at least machines running Windows--they may be the x86 Macs). If you're talking about console-based applications then you can write stuff in C and all you need is a compiler to run it on different OS's. Most educational curricula tend to focus on Java since it's an easy language to learn and play around with, but for most real-world purposes, Java doesn't really cut it.
Having real engineers teach classes is probably something that most high schools can't afford, so that is pretty cool. However, I think they are doing you a great disservice if they intend in any way to suggest that Macs are the be all and end all of computer systems when it comes to engineering. In fact, I think it is more likely that they are part of Apple's discount program. My school back in Indonesia was part of the program and all we had were PowerPC's.