I think so. On June 10, 2000, I presented my paper Hands-on Computer Architecture - Teaching Processor and Integrated Systems Design with FPGAs at the Workshop on Computer Architecture Education at the 2000 International Symposium on Computer Architecture in Vancouver, BC. My slides are here: WCAE00 slides.

"Why build an undergraduate architecture course around FPGA-based processors and systems? Because there is such value in the experience of building real hardware. Besides the emotional appeal of booting a computer made of your own ideas and your own hands (and how many educators have had that pleasure?), FPGA CPUs can impart a realism to the learning experience that is probably not available in more textbook or simulator-based approaches."

"So much of computer architecture is about making tradeoffs such as performance versus area versus cycle time versus power, etc. While there is much value in a course project to develop a processor model in an HDL, and then study its behavior in a simulator, it doesn't go far enough. It's like teaching how to balance a home budget but with a bottomless checking account. By not closing the loop with some kind of realistic cycle time, area, and resource-usage data, the design tradeoffs aspect suffers."

Check it out - in particular, the last two pages on "advanced computer architecture research" list some FPGA computing research topics.

[updated 02/18/01]
For an interesting student perspective on this kind of project, please read How the Puerco was born.