I have a virtual machine with WIndows 2008 installed.
If I wanted to determine whether it is the VM settings or host that is causing the problem, what sort of counters and graphs should I look at?
Also how would I determine if the datastore where the VMs are stored is the cause?
You might also want to try using the Performance Troubleshooting Guide here:
you want ot look at the davg counters
This video should be a great starting point for understanding the key vCenter metrics. It tells what the key metrics are, what they mean, and how they'res used. Let me know if it helps or if you have more questions.