Well, I'm still in school kinda and I'm still in the planning stages of my startup, but I feel that I learned a lot of stuff in college that I really wouldn't have touched otherwise. I dunno how practical it is in the "real world," but I thought my time/ money was worth it.
Compilers and languages -- Right now I've got ideas on how to create a new and better programming language (hopefully that will be the 100-year language =P) which will have stuff from lisp, prolog, C++, Java, and first order logic. honestly, there would be no way that I would try to learn lisp by myself, much less understand the elegance of lambda calculus. I wouldn't know where to start thinking about other complex things like knowledge representation and complexity related to it.
Linux / vim / eclipse / makefile -- I picked up how to use a lot of tools in college, when some other friends also used it. It would have really bad if I had to learn all of those without being able to call someone up and ask for help.
networking -- I've done some stuff outside of school for a year that had nothing to do with CS. I really haven't met so many "simple" people before... not that there's anything wrong with that, but I really do not think of them to do interesting projects with. Not all the people I knew from college was a CS major, but I can see myself working with a lot of them for various projects.
Machine learning -- This was one of those things that I was interested in, but I can't see myself learning about it all by myself. I took a class about it for audit, then took it again a few years later. It really makes a difference to be pushed to do the work. And even though I forgot about a lot of the details, I don't think it would be too hard to re-learn about random forest, bayesian networks, reinforcement learning, etc.
It seems to me that there are a lot of software companies out there that do some stuff that are pretty heavy on the theory side. Google's pagerank, spam filters, antivirus software, etc. I'll bet those kinda jobs are better than a "4-year-experience-with-java" job.
I'm also not too sure about the "replacing college with an incubator" thing... college is something you gotta do, doing a startup is supposed to be a risky thing. I've done a year long senior project that I just totally blew off because it was a "class project". People have done much more stuff in three months than what I did that year. If people see the startup incubator as something that's required, i don't think it would work out as well. But I think it would have been helpful if there were more incubators that were closely tied with the school, so that it wouldn't seem like such a far-fetched idea to do a startup.
btw, those humanity classes really are a total waste of time.