The one thing that hasn't been said yet in this post that rings true in every certification agency debate is: The instructor makes all the difference!
Find an instructor that is thorough, makes sure you understand the skills and risks and makes sure you have fun. That instructor could be a PADI or SDI or SSI or YMCA or NAUI instructor. Most agencies recognize each other and allow cross-overs.
Now that I've said all that objective stuff: I'm a PADI diver because they are the largest and my card is recognized when I travel to that out-of-the-way dive shop in who-knows-where. My PADI instructor was extremely thorough for both safety and liability reasons, which you have to respect. Also, I like the fact that I can use tables to dive. Some agencies allow you to train with a computer and don't require you to study dive tables or give you as thorough an understanding of decompression theory. If my computer ever quits on Monday of a week-long dive trip, I can continue diving the whole week by working the tables.
I'm not trying to fuel the fire or slam any other agency, I said all that only to share with you my reasoning for choosing PADI.