Your shortlist should have a uniform mix of rankings i.e. choose 2-3 universities in the top 10, 2-3 in the top 50 and 2-3 lower than that. Based upon your honest assessment of your personal ability, you can reduce or increase the number of univs in any category. Your final shortlist should reflect this. Remember, usually only about 50 - 75% of the universities you sent a pre-app to will reply (in time). So you need to send many more requests than you intend to actually apply to. This is not the case with Internet based research, though. You can get information on as many universities as you desire - fast and guaranteed. So you need to search lesser universities.

You also need to determine the reputation of universities in your field of interest. Ask your friends, faculty, current students, people in the industry, and if you can, recruiters.

Go through the list of degrees and courses offered at the university. You may have to check different departments with similar courses. For instance, at Carnegie Mellon, you can get a degree in a Computer related field in the Engineering School, the School of Public Policy, the School of Computer Science, the Information Networking Institute and more ! Each has its own course structure, its own focus area, its own fin aid options. To find such detailed information, you could check out the comprehensive university handbook at USEFI, or visit the university website. Click here for a list of websites.

Also see presence of research labs with adequate funding (useful for fin aid) and see faculty research interests, including papers written by them. If you are using the net, all this can be done at the pre-app stage itself. If you're writing to univs for an app packet, then do this on receiving their brochures.

Check whether the university offers financial aid. See the total annual research budget of the university, the percentage of incoming students who are offered any form of aid, and whether aid is available for the program you are applying to (e.g. while Carnegie Mellon offers aid generously to almost all incoming students, applicants to the MSIN degree are given none). Be careful. This could be an expensive mistake. Email current students, faculty and the admission office of the college about this.

Finally, look at the total cost of attendance of the course, if there is a possibility that you are not offered any financial aid. This cost includes the tuition cost and cost of living for atleast one year. In most multiple years courses, you can get a job or assistanceship after your first year (or even first semester), so you needn't worry about further costs.

There are many other parameters like climate, number of international students, closeness to big city etc. which may also be used here. But I think that those I have mentioned above are primary. If you feel the need for any more factors, feel free to add them. After you have shortlisted your universities, a table of this sort can be made to keep track of the details of each.