If you already have a Nexus, or would be comparing off-contract price of the two, the Nexus is a compelling argument, especially after the Jellybean update. However, if you're buying on contract (say, because you used your last Verizon upgrade), or have the money and don't mind the full price of the S3, or simply bought the phone because you want the best for now and are excited about it, S3 is the way to go.
The Jellybean update looks great, but its not like its a Nexus exclusive. A Nexus device will always get updated more quickly and have stock Android, everyone already knew that. The arrival of a new version of Android may make it more compelling right now, but Jellybean will come soon to the S3. Sure, it'll be a while before Samsung brings the update to the S3, but I expect we'll see good AOSP JB roms for it by the time the OTA rolls out for the GNex, so it'll definitely be an option.
Remember, Samsung made both units, and the S3 is their flagship and 7 months newer, so you do the math.