All of the certifing agencys are just about the same for their basic scuba class and even their advanced class. The way they teach varies a bit from agency to agency, but they all have to teach the same stuff.

The difference is more between different shops and more importantly different instructors. Your best bet is to try to meet with a few of the different insturctors to get a feel for whom you like the best.

Now in a final word, I am NAUI certified, and my wife is SSI certified. We were discussing getting going for our Dive Master certification so someday we may be able to work in diving. The more we thought about it, we decided we should go with PADI. Now, I perfer to go with a more technical based agency, but the bottom line is if we want a job in SCUBA, PADI is the biggest worldwide and will have the largest job availibity. I have never gone on vacation to see a ANDI or SSI or TDI dive shop, but I always see PADI.