There are various different certifying agencies. I'm NAUI certified, but there is also PADI, SSI, and YMCA among others. There is no real differece that I've noticed except for in the dive tables (YMCA being the most conservative I've noticed in times with longer dive intervals/shorter bottom time and PADI the most liberal with shorter intervals/more bottom time). Most excursions I've been on use PADI tables, but I've encountered a few that use NAUI tables.

The skills you acquire will be the same however. My tip, the swim test isn't a race... have fun with it. Any stroke, take your time and be consistent. I floated on my back for 10 minutes during the water treading portion, and then just kicked my feet for 200 meters for the swim test