I have to concur with miesemer -- which instructor and which dive shop are far more important than which agency (and I am an SSI instructor). Your goal is to figure out which of the local dive shops will treat you the best and which instructor is going to put the most effort into making you a safe, confident, comfortable and competent diver. That's easier said than done.
When it comes right down to it, the differences between agencies are subtle. They all ascribe to a set of minimum standards that a new diver must meet to be certified. The real measurable difference comes from the way you are treated by the store and the instructor. Some are just mills churning out new divers like low grade lumber. Others are truly interested in helping you make the most of diving.
Ask lots of questions and see what happens. Do you get a meaningful dialog, or do they just keep preaching to you and trying to sell you something? If they're convinced they know everything and just want you to accept that carte blanc, then walk away. If they're willing to spend time with you giving you real information and trying to learn more about your interest, then that is likely true in the classroom and pool, too.
Sometimes it helps to pay attention to the other customers in the shop, too. Are they all interacting and having fun with one another? Or is it more like a Walmart where they're just strangers shopping under the same roof? The more personable stores and instructors that take serious time to develop relationships with their students/customers will be easy to spot just by way of the relationships demonstrated between staff and customers on the sales floor.
Another thing to look for is whether or not there is any follow-up in the store. Do they have a dive club? Do they put together group trips? Is there any evidence that people are sticking around after they've been certified? Find out when the next dive club meeting is and drop in for a visit. Ask the other club members which instructor certified them and how they felt about him/her. PS: If no one shows up for the dive club meeting, that's a fair indication there's a problem.
Anyway... these are just a few tips. Hope they help some.
Edited for glaring typos