Modelling Virtual machines has been a popular option for many software inventions. Sun's Java Virtual Machine is regarded as benchmark implementation of virtual machines.

However, you can find many VMs being developed based on Sun's implementation. IBM's Jikes VM is a popular implementation of Java Virtual Machine, which has been completely written in Java language. There are many papers explaining the implementation and design prinicples. (more)

Check out this, virtual machine viewer. Basically it is method, instruction tracer.

And finally, if you are suffering from threadaches, Sun has prescribed this article for all its developers.