3D Printers should be used sparingly and wisely.
At the industrial design school I worked at, students were introduced to 3D printing during a 40-hr class in the first or second year, including a visit to a 3D printing service facility. The number of 3D printers and access to them is limited, the high-end printers only being available to master students. There has to be good instruction on what type of prototyping process to use, before students limit themselves to just 3D modeling and printing, straying away from hand modeling which is enormously valuable as well both as creative tool and prototyping method. Then for creating experiential (visual+functional) prototypes there has to be good instruction on what type of process to use as well. Stimulating students to plan ahead and use an external service agency such as Shapeways for their prototypes works well too.
Because education becomes more and more diverse, multidisciplinary and tailored to the individual student I vote for ideas such as awarding students with 'expert points' that they can trade in for using certain machines or doing special workshops, when availability is limited. It will also be an incentive to produce better work when that allows them to gain more points.