The Parrot is an upcoming virtual machine that will be used for Perl 6 along with other dynamic languages such as Ruby, PHP, Python, to name a few.
Parrot is a little different from the Java Virtual Machine and Common Language Runtime as it is a register-based VM rather than stack-based like the JVM and CLR. Here's a bit from the Wikipedia entry on the Parrot virtual machine:
Virtual machines such as the Java
virtual machine and the current Perl 5
virtual machine are also stack based.
Parrot developers see it as an
advantage of the Parrot machine that
it has registers, and therefore more
closely resembles an actual hardware
design, allowing the vast literature
on compiler optimization to be used
generating code for the Parrot virtual
machine so that it will run bytecode
at speeds closer to machine code.
Although it may not be exactly what you're looking for, there was news of an interesting use of the Low Level Virtual Machine (LLVM). Adobe has a project called Alchemy, a C/C++ to Flash bytecode compiler, which utilizes the LLVM's optimization facilities to produce well-optimized Flash bytecode, according to this Slashdot article.
I think we're going to see more interesting uses for virtual machines, and increased adoption with better optimization and on-the-fly compilation techniques, along with the increased amount of computing power which is becoming available with newer, faster processors.