Contemplating this PhD business. I did my undergrad in the midwest and kind of want to do grad school by one of the coasts. Anyway, let me know how you made your decision.
How you choose is going to depend at least somewhat on why you are going.
If you are doing academia then the relative prestige of the school you go to and the professor you work with will have an impact. If you are going industry that is less true.
The second piece is what exactly you want to study. Knowing this will make a huge difference in your search and ability to get accepted.
Look up research papers in the area that interests you. When you see papers specifically on areas that interest you look up the professors involved. They will usually have a site with their research interest, current students, and possibly the lab they work in within the university. The lab may have other professors and other students associated with it. Check those people out too. Then start contacting professors. Explain your situation, your interests, how their work intrigues you, etc. What you are looking for is whether or not they might have room for you to join their team in the coming year. Even if they don't it probably won't hurt to apply at the school.
When I worked as an RA we had two people join the lab. While they had to apply to get in it was really a formality as the professor had already said he could get them three years funding each. I'm sure other schools work differently so ymmv.
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