In virtual box 3.0.2 is there any performance difference between using the native VDI virtual disk format and the VMDK virtual disk format?
I don't think so - for example, this blog post claims the following:
Both formats are wrappers around a raw disk image so raw performance isn’t really at issue.
However, it also says the following:
VirtualBox has to mount a vmdk image as a writethrough disk, which means it loses things like snapshots and possibly driver performance.
I don't know if this applies to the newest version, but it sounds like you should go with VDI.