VMware is closed source. The real Xen alternative is KVM. KVM is better than Xen in pretty much every way. There's a very big cost for big Xen shops to switch to KVM, but if you're not tied to Xen I can't imagine why you'd use it when KVM is better in every way (kernel integration, tooling, performance, etc).
With that being said, there have been exploits in the Xen hypervisor. As more hardware integration gets added, dom0 starts to look a lot more like a traditional kernel.
Personally, I use kvm for all my virtual machines, since I don't want to run everything under dom0.
Did you mean Xen?
Except for every single "prepackaged developer's workstation" solution I've seen so far. Seriously it works on all systems more or less the same, so I see it used all over the place.
Xen is meant for running a potentially large number of server VMs headless. VirtualBox is meant for running desktop VMs. You could make VirtualBox run headless (exposing a pseudo-screen over VRDP) to do what Xen does, but... eww.
Qubes is awesome though. It really does not get as much attention as it deserves.
Just look at the kinds of vulnerabilities regularly found in it. They're mostly run-of-the-mill buffer overflows or missing range checks in emulation. Simple stuff that should have been caught if they were serious about security.
Compare that to xen or kvm, which have of course also had vulnerabilities, but you can see people usually have to get a lot more creative when attacking those.
If you wouldn't run a program on your actual machine, you probably should not run it in a VirtualBox VM either.