https://github.com/onetrueawk/awk - UNIX philosophy of small tools, DSLs, CS theory: state machines / regular expressions, Thompson algorithm ...
https://github.com/mirrors/emacs - Both a program and a VM for a programming language, hooks, before/after/around advices, modes, asynchronous processing with callbacks, ... Worth to think of challenges of designing interactive programs for extensibility.
https://github.com/rails/rails - Metaprogramming DSLs for creating powerful libraries, again a lesson in hooks (before_save etc.), advices (around_filter etc.), ...
https://github.com/git/git - The distributed paradigm, lots of CS theory again: hashing for ensuring consistency, DAGs everywhere, ... By the way, the sentence "yet the underlying git magic sometimes resulted in frustration with the students" is hilarious in the context of a "software architecture" course.
One of computer algebra systems - the idea of a http://en.wikipedia.org/wiki/Canonical_form
One of computer graphics engines - Linear algebra
...
There are loads of things one can learn from those projects by studying the source in some depth, but I can't think of any valuable things one could learn by just drawing pictures of the modules and connecting them with arrows. There are also several great books that explore real software design issues and not that kind of pretentious BS, they all come from acknowledged all-time master software "architects", yet all of them almost never find diagrams or "viewpoints" useful for saying the things they want to say, and they all walk you through real issues in real programs:
http://www.amazon.com/Programming-Addison-Wesley-Professiona...
http://www.amazon.com/Paradigms-Artificial-Intelligence-Prog...
http://www.amazon.com/Structure-Interpretation-Computer-Prog...
http://www.amazon.com/Unix-Programming-Environment-Prentice-...
http://www.amazon.com/Programming-Environment-Addison-Wesley...
To me, the kind of approach pictured in the post, seems like copying methods from electrical or civil engineering to appear more "serious", without giving due consideration to whether they really are helpful for anything for real-world software engineering or not. The "software engineering" class which taught those kind of diagram-drawing was about the only university class I did not ever get any use from, in fact I had enough industry experience by the point I took it that it just looked silly.