When it comes to course enrollment/registration in a limited-enrollment course, most institutions use a sequential system where students pick their course schedules sequentially (often ordered by seniority, then first-come-first-served or randomly within groups with the same seniority). Some institutions, particularly business schools, use "bidding mechanisms," where students bid (in bidding points, not real money) on the opportunity to take over-demanded courses.
These have their advantages and disadvantages, but it seems like there ought to be other ways to handle course allocation. For example, a university might use a system like a sports draft, in which people pick just one course at a time. Are such draft systems actually used and are there other interesting non-standard ways of handling registration for restricted-enrollment graduate or undergraduate courses?
A clarification: By sequential mechanisms, I mean mechanisms in which students one-by-one select their full course schedule for the upcoming term. Obviously some systems allow a group of students to register within a given window. I still count this as sequential as it is processed sequentially: the order within that window is determined by the order in which the students in that registration window submit their requests. In economics and mechanism design, this is typically referred to as a sequential dictatorship (or a serial dictatorship, which is slightly different only in that the order is predetermined and not dependent on previous selections).