The MS EE program offers a great deal of flexibility in terms of which classes you take: As long as you complete 30 credits of graduate level courses, subject to the other relatively mild constraints specified in FAQ on MS Requirements, you get your degree.
Given that, your choice of courses should reflect your goals in studying for the degree in the first place. In particular, if you have some particular area within EE that you wish to focus on, you will likely put together a set of courses related to that area. In addition to depth in your main area of interest, you will probably also want to fill in breadth in associated areas.
Frequently there will be specific advanced courses you wish to take, but they will have other courses as pre-requisites. Since most courses are offered only once a year, you need to plan to make sure you will be able to complete the pre-requisite and target courses in the correct order. The Graduate Course Charts summarize graduate courses by area and conveniently show the pre-requisites. The course lists for the current and past semesters give a fair indication of what courses will be offered in the future.
To help develop rounded programs, the faculty have put together a number of concentrations, which are suggestions of sets of courses that make a consistent whole. You are however completely free to ignore these suggestions, and concentrations have no formal role in your degree (they do not appear on your diploma). See the FAQ on Concentrations.
Finally, remember that taking a class is a good way to get to know a particular professor. If you are thinking about trying for the Ph.D. program, or if you just want to make a contact for possible help with your career (such as letters of recommendation), the easiest way is to take a course with a particular professor, and impress him or her by excelling in the class. Of course, normally the professors who are of interest to you will also be teaching the classes that are of interest to you.
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