It is also worth noting that the Java launching mechanism changed between Java SE 6 and Java SE 7, along with the vendor change from Apple to Oracle. This means, among other things, old Java .app bundles need to be re-bundled to work properly with Java SE 7, and not insist on using Java SE 6. The Eclipse IDE and LibreOffice are two prime examples: The current stable versions of both these applications needed repackaging (and in LibreOffice's case, a recompile for 64-bit as well) so they'd detect and use Java SE 7, and furthermore will actually function without Apple's Java SE 6. The developer builds of both of these (Eclipse Luna milestone builds; LibreOffice 4.2.0 64-bit Mac betas/RC builds) do work without Apple's Java installed at all.
One more thing to note that caused headaches for developers of all sorts using Java: When Oracle released Java SE 7 for Mac, support for 32-bit was dropped. This in turn means that Java applications relying on 32-bit libraries need more than just a rebundle to work in an environment lacking Apple's Java.