I understand that the Oracle Java SE contains closed source extensions and tools that are not part of the OpenJDK however is the Oracle Java SE JVM identical to the OpenJDK JVM or does Oracle make changes to the OpenJDK JVM before releasing it as a Java SE JVM?
Update 1:
I found some info from the JDK7 updates projects: http://openjdk.java.net/projects/jdk7u/qanda.html
Will the 7 Update Project receive security fixes from Oracle?
Yes.
As with OpenJDK 6, security fixes are first kept confidential and applied to a private forest before being pushed to the public forest as part of the general synchronized publication of the fix to effected JDK release trains. In addition, they will not go through the public code review and putback approval process, and their corresponding issues in the Project’s issue tracker will not be publicly visible.
OpenJDK is the reference implementation of Java as of version 7.
OpenJDK 7 is the starting point for the version that Oracle distributes as Oracle JDK. Other vendors (e.g. RedHat for IcedTea) may also use OpenJDK as their starting point.
In terms of the differences between OpenJDK and a vendor VM, there may be patches which a vendor wants to apply but which the overall OpenJDK community has not accepted into mainline.
Vendor VMs must, of course, be able to prove that they are in conformance with the TCK if they want to use the Java trademarks to describe their product.
Oracle JDK is also not open-source. This is possible because of Java’s dual licensing arrangements, and the fact that Oracle own Java overall.
Do you have more specific questions – as posed, your question is a bit vague. What specific aspects are you interested in?