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Just to get the last word in The Raspberry I has 17 GPIO pins.

Uno all the way. The LIFA toolkit is pretty neat and there are some libraries in there I didn't know were supported (I2C, SPI are a couple) I wrote an application using the NI 8451 to do all my SPI communication. When I was done I found the LIFA toolkit supported it. So I dropped in the LIFA VIs, commenting out the 8451 VIs, and my application worked just as well. You mean I could have used an open source $13 piece of hardware to do all my SPI communication instead? We still went with the NI solution for support, and all the other goodies but the next time around, I may budget to use the 8451 but actually use the Uno. We've also used the Mega but I think very few applications actually need the extra memory it comes with, really it's just for more I/O. You can even get an Uno and LabVIEW (Student edition) for $50 on sparkfun. One thing I would recommend for anyone who has a bunch of Arduinos, use XLoader to flash them with the LIFA instead of the IDE. It is faster, and it only takes a few clicks.

Unfortunately I can't help you much in this regard as I've only used it in a standalone application (a sous vide cooker currently). However, a friend of mine at NI put together a LabVIEW Interface for Arduino awhile back that does exactly what you are wanting if LV is an option which worked well when I first got it and wanted to try it out right away. It just uses VISA commands though, so you could start there if you didn't want to develop the c/c++ code. As far as hardware goes, this kit was a pretty good deal IMO and the ultimate one might be perfect for small classroom projects.

Uno's are great, cheap, and plentiful. If I were choosing a model to introduce students to, that would be it. I use the Due more myself, mostly because it coexists in my 3.3V ecosystem. It is so easy to plug 5V into a 3.3V input and most of these cheap boards are very intolerant of it. For students it is good to be on the safe side. Added bonus is that the microcontroller is socketed on my Uno's which makes them easy to replace. And the Uno's USB performance is quite good these days, and the issues before are mostly using firmata in firehose mode (spray data until a buffer overflows), the digital i/o toggle mode is quite robust in my experience. Usually I can set a pin and then query the pin to verify the setting. And in this case you are right, I envision the firmata sketch(ships with the arduino ide) installed on the arduino and the other code (LV, python, java) on the host computer. The A students could program the microcontroller directly for extra credit.

While not directed at me, I've been using the Uno and like it quite a lot.

Well, thanks to the LabJack ads which are now following me around the internet, I see that it is $108. That's a lot of arduinos, and more than I paid for my USB-6009 on EBay. And if python were an option, pyFirmata is available, and while it is still missing a few of the latest firmata changes, driving a digital port is its bread-and-butter.

Have you look at LabJacks http://labjack.com/ not as cheep as the Arduinos but there are Java drivers and a some level of Java support forum, or maybe a Raspberry Pi http://www.raspberrypi.org/

There must certainly be a firmata library for java by now (a fine exercise if not), and that would allow an Arudino to easily become your USB digital i/o module. With Arduinos running me about $6 on Ebay (not that I need more bidders...), that seems to fit the low-cost bill.

Okay I don't think I'm as bad as some of you guys but I too find my self moving things one pixel at a time some times to line them up nicer. But there are a few times that I hate the terminal choices used by NI. Here are two times that I can think of that irk me. Why do these not line up? Seriously NI? Seriously?