Determine which things matter the most to you in choosing a school. There are some things that will extablish whether you can consider a school at all, like whether it only accepts applications from certain groups or from people with certain previous degree and experiences or whether the application deadline has past. Other things that might affect your interest in a school are the price, style of education, reputation and required test scores.
Gather information from the schools' about the programs they offer. Their websites may have a lot of the information you're looking for about their tuitions, courses and application processes, but you may need to request a mailing from or call some online programs to get more information about their schools.
Seek out additionally information from other sources. There is some information schools might not be eager to share about themselves, and outside sources will always give you a better sense of where schools are stronger and weaker than one another. Websites like elearners.com and worldwidelearn.com have information about a number of online master's degree programs and universities, and collegeboard.com's in-depth reviews of schools' information and statistics cover these programs too.
Make sure the schools you are considering are legitimate and accredited, particular since it's easier to fake a school that takes place online. Check that schools have real coursework and faculty and aren't simply selling a printed degree. The department of education has information about which accreditation groups are legitimate, and those groups have information about what schools they have accredited.
Keep a spreadsheet or other document with information about each school you're considering applying too. You can rule out schools that don't fit your needs, though you may want to save the information if you needs could change in the future. You may decide to apply later to a school whose current application deadline has past or your financial situation could change. Prioritizing the schools that are left will allow you to transition from comparing programs to applying to them.