The virtual machine for Smalltalk is quite simple. It contains a set of primitive instructions that directly reference Smalltalk code. This makes the virtual virtual machine easy to connect. Therefore, Squeak is often used to experiment with a virtual machine.
Pharo is a project to replace the Squeaks core library, as Squeak's appearance is somewhat outdated. It uses Squeak VM and is mostly compatible, but the interface is completely different.
On the side of the VM Squeak there is a vanilla VM. As far as I know, this started as part of the Squeak project and is still in use.
Then, some time ago, Eliot Miranda, a researcher at VM, announced that he was developing a new optimized virtual machine for Squeak. Cog is open source and can be used with Squeak and Pharo. It is still actively developing, but faster than the underlying virtual machine.
Newspeak is a completely different animal. This is an experiment to create a language that uses a clean message passing as the only primitive of the language. It is based on Squeak VM, but not really Smalltalk. You can find more information about this at http://bracha.org/Site/Newspeak.html .
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