I'm not sure if there's been any changes regarding signing, but I can confirm that VirtualBox has been working fine through Vagrant for me.
VMWare has an early access Fusion update that works, you can download it from their support site. Works okay for me so far.
They do. This broke Viscosity VPN software for me between DP3 and DP4, and the Viscosity guys say they are waiting for their key to be signed before they can release a new beta.
This also broke AT&T AllAccess (software for my LTE USB modem).