I've been through the PPC to Intel migrations so many times for so many school districts that I'm still fairly amazed at how well it usually went as long as the apps weren't trash.
The biggest issues I ran into was always with the low quality edu based applications. So many of the issues we had with those apps were because they were created in Windows and ported half way to OS X, an old PPC version that did something special that the Intel version couldn't do, or the worst one using a special baked in version of Adobe Flash..
I've been out of the edu game for a while now. I want to say it was the Map Testing system. The school district was using a web based system (something lightning? I can't remember) previously, but the state was mandating the use of MAP instead. The state didn't give the schools any options or much time to prepare for it either. The school district had 70+ schools. I spent a summer fixing / getting that stuff working. (still more fun than iPad deployments)
The app wasn't a universal binary at the time. Which would be fine if the PPC version worked with the PPC machines, and Intel worked with the Intel machines. haha.
*Edit
The windows version did usually work without issues. The OS X version eventually worked once they redid the whole application.
Edit: maybe I should explain a little. We were a educational software developer and doing multimedia titles. We had a home grown multimedia engine which served us well (at the time there weren't alternatives) but Flash came along and at the time they would license the engine as a C or C++ library, which we could embed. This would get us a capable engine with superb integration with the content creation tools.
phew, I was hoping MAP wasn't going to come back to haunt me after all these years, haha.
If your application let students finish what they were doing without randomly crashing and losing everything, then it is leaps and bounds better than the MAP system.
The school had to extend the map testing by 2 weeks just because of how often it crashed and students had to retake it. My coworkers at other school districts in other states ran into the same exact issues. Then on Windows, it had to access a SMB share somewhere to dump data to a flat db... that would get corrupted sometimes when a students application froze up... haha. it was job security though.
The biggest issues I ran into was always with the low quality edu based applications. So many of the issues we had with those apps were because they were created in Windows and ported half way to OS X, an old PPC version that did something special that the Intel version couldn't do, or the worst one using a special baked in version of Adobe Flash..
/shivers