They are all about the same. Slight variations in content, but physics is physics and there ain't not way around that. So the real differences are in the presentation and follow-up course availability.
PADI, NAUI, SSI all good. PADI is probably the undisputed internationally recognized organization that does have the quick-certcheck capability. SSI has a toll free number as well. Not sure about NAUI. Bottom line is, don't forget your card when you go. Keep it with your mask/fins/snorkle/booties (all your personal gear you probably want to own) and you won't have a problem.
FYI- I was an asst. instructor for PADI and SSI, divemaster for both, and a boat-load of speciality certs. Originally cert was NAUI.
Final recommendations include go with your certs BEFORE your trip. It will be much better to get it out of the way before hand and have an idea of what to expect when you do it for real. Second, go with a shop that is convenient to your location. If it's PADI, and close and you like the people, go with them. If it's SSI or NAUI, go and meets the criteria, go with them.
Scuba is a great sport and you should choose your shop like you are going to build a long-term business relationship. The more you frequent, purchase and service, the better they get to know you and associated treatment and favors/discounts.
My .02...
~m38a1