You can develop a rubric to apply to a selection of papers if you want to address, for example, critical thinking. Students are charged a fee for the writing exam and portfolio assessment, and we pay graduate students a stipend to keep the database in order during the summer. It depends on institutional culture, but there wasn't a lot of opposition, and consensus building developed slowly. It helps them see the links between courses they take and provides them with work samples that can be used for job applications. The logistics don't need to be complicated.
Students collect their own material, in a special envelope.
They spend a couple of hours putting their portfolio together. They make the choice. A writing course is available for students with weak portfolios. Ours is set up as a mid-career assessment. Portfolios in that category get an additiona reading. .