First off, a rant. Either your Computer Science program/dept does not truly deserve the name or you did not fully attempt to master the curriculum as it is intended. I know it sounds harsh, I am mostly annoyed by the constant misconceptions about CS that pop up here on /. from time to time.
A masters degree in Computer Science builds upon the basics of theoretical CS (theory of computation, languages, grammar, logics, discrete math...), technical CS (microcontroller, assembly) and applied CS (functional, OO and logic programming) from a undergraduate CS degree and extends it with topics about Networks (Sockets, Protocols, OSI Layers, Routing), AI (both classical AI with logic, planning and formal systems as well as machine learning), Operating Systems (for instance reimplementing parts of and studying Tannebaums Minix, Filesystems), Databases (Tuple relational calculus, OO databases, inductive databases, knowledge discovery) and also, and this is what I think you definitely missed out on, Software Engineering. This would involve developement models (V-model, Waterfall, extreme programming), UML, testing, maybe software verification, refactoring and so on.
Note that there is not much hacking (in a positive or negative sense) involved here. Great hackers do not necessarily need to be computer scientists, and competent computer scientists definitely do not need to be or leave the university as any from of hackers (be it some low level C pointer wizards or some OS file system experts).
I think what you meant to say is that the university did not teach you how to code in an industrial/enterprise setting. And rightfully so, thats the job of a vocational/trade instituion, but not of an university.
However, let me give you some pointers that helped me to grasp a bit more beyond purely academic programming.
1. Patterns. As some others have pointed out, this pretty much a must to grok in any OO project. The Gamma book is good, if you are looking for some really good intermediate more applied Java book about this, Effective Java by Joshua Bloch (he developed, among other things, the Java Collections).
2. Revision control management. One word: git. Anything beyond toy problems should not be touched without revision control. Watch the video with Linus Torvalds (the creator) to get motivated: http://www.youtube.com/watch?v=4XpnKHJAok8
A pretty good git tutorial that I like can be found here: http://www-cs-students.stanford.edu/~blynn/gitmagic/ch01.html
3. Read competent peoples code of the language of your choice! github and gitorious are a real treasure. The more you do it, the more you will discover more efficient approaches of how to implement certain concepts. And you will also see a lot of bad code and learn how to spot it.
4. Testing. JUnit is pretty basic to grasp. Some people swear by TDD (test driven development, write the test case first and then the implementation of what to test), I find this a bit extreme, however unit testing is a must to know.
5. Program yourself! Pair programming can be very helpful if your mentor is knowledgable and able to teach, otherwise do it yourself. Do not hack for the hell of it (although it can be fun), but focus instead on clean and clear concepts that you want to implement and improve upon. And document your code (doxygen or javadoc are your friends).