The University of Wisconsin Oshkosh have an interesting "University Studies Program" supported by an e-portfolio. There is a slideshow "University Studies: embedding High Impact Practices and ePortfolios at UW Oshkosh" by R. John Robertson, Educational Technologist at UW Oshkosh explaining approach.
As I understand it (from reading the USP Instructors Guide), as well as learning outcomes for individual courses, there are ones for the program (in the liberal arts). In addition to matching assessment to the learning outcomes for a course, designers also provide a reflection exercise on a key assignment, which matches some learning outcomes for the program overall. Students can then add these assignments to their e-portfolio, to show evidence of having achieved the program learning outcomes. This allows students to choose from a range of courses, but still meet a common set of program requirements.
Outside the liberal arts, this approach could be useful in programs which are accredited with professional bodies. It can be difficult to meet some of the professional skills requirements,within the confines of a course based program. The e-portfolio approach allows students to indicate where they have met the requirements.
UW Oshkosh have taken a systematic top-down approach, where course designers nominate assessment items for the program objectives. But this might be done in a more ad-hoc way, where students themselves identify where the program objectives are covered in courses. This would require some education of the students about what objectives are and how to provide the evidence. But this would avoid having to change all of the hundreds of courses typically offered by a university. It could also be used by an external accreditation, with courses from multiple universities.