The major use case for these was for number crunching (training neural nets, running physics simulations, etc). And these things were something crazy, like 100x faster than a similarly priced PC server. There were plenty of libraries out there for doing linear algebra.
A quick google search suggests that this was extraordinarily common in academia. I found materials from lots of different universities that were close to what I remember my peers talking about.
This was also a little bit before CUDA hit. So there really wasn't a mainstream offering for doing massively parallel, SIMD calculations.
Edit: I went to Wright State Uni and most of my CS professors did research associated with the Air Force, which as forgotpwd16 notes, had at the time a super computer made from PS3s. This might explain why the PS3 was so popular among our department.