It seems to me that there was a time that a lot of the Software Engineering work was contributed by Universities. Operating Systems, Databases, Compilers, Networks, etc. Examples that come to my mind are UCSD Pascal, Unix Berkley, Ingres at Berkley, Kermit Project at Columbia. I don't see that any more. You should be able to get a PHD by designing and implementing a state of the art piece of software. Even google was started as part of a research project I think.