I can imagine that Apple Java might be better tuned for Macs but Oracle Java might be more active development. I'm specifically wondering about video and 3D performance for Minecraft.
1 Answer
There is no "Apple Java", Java for OS X is maintained by Oracle.
Even Apple's page about Java says that you can get it from Oracle's java page.
Also if you are wondering about the old Java SE 6, it is old, and should be used if apps specifically require that.
Also, Minecraft uses Oracle Java.