It comes down to personal preference.
The Galaxy S3 has a lot more features built in (motion control, s voice, all-share, built in apps and widgets, etc) and has better hardware (faster processor, more RAM, better screen, better camera).
But a lot of Android enthusist don't like the TouchWiz interface that Samsung put on top of Android and don't like all the bloatware that come preinstalled. The Nexus gives you a pure Android experience with no bloatware, which is imporant to some people. It also will get faster updates (although it should be mentions that updates still won't be as fast as the GSM Nexus). Also if you're into rooting and flashing custom software, the Nexus is much more hackable. But really the Galaxy Nexus is running on last year's hardware, although thanks to JB it's running very well.
Edit: but a lot can change in a few months. There's rumors of a new Nexus device coming "soon".