There are nearly as many theology schools to choose from as there are ways of looking at God, and choosing from among all the options can seem overwhelming. The route you take will depend largely on your purpose, whether it is to become ordained, to pursue a scholarly career in theology, or to gain personal or practical knowledge. Generally, you will need to choose from an undergraduate, seminary, or certificate-based program based on your reason for attending.
Probably the most common motivation for going to theology school is to become a member of the clergy in some religious group. If this is your reason, you will probably choose to go to seminary, which is a graduate-level program. Some religious groups also ordain people with undergraduate theology degrees. In general, you will need to investigate the requirements of the particular group or denomination by which you want to be ordained.
If ordination is your goal, chances are you already have some idea of your own theological beliefs. You should consider which of those beliefs are most important to you, and how important it is for you choose a theology school that matches those beliefs. Conservative theology schools tend to hold more closely to the historically accepted tenants of the faith they represent, such as the literality of canonical texts. More liberal schools, on the other hand, may not hold as strictly to these beliefs. Of course, "conservative" and "liberal" refer to opposite ends of the spectrum; in reality, most theology schools will fall somewhere in the middle.
On the other hand, if you are interested in a scholarly career theological career, your needs may be slightly different, although you will probably still choose a seminary. In this case, your method for choosing a theology school might be very similar to choosing any other graduate education program. Chief among the factors to consider might be the research interests of a school's professors as well as your own opportunities for research and publication if you should attend. You will also want to consider opportunities for funding through various assistanceships.
Some people want to get a theological education not for professional advancement, but for personal knowledge to apply to ministry situations. In this case, non-accredited theology schools might be worth considering. These programs may offer some sort of certificate for completion, but no actual graduate or undergraduate credit. A non-accredited program is likely to be by far the least expensive option, and may provide more practical rather than theoretical knowledge.