Is there any best practices guides or documentaion for optimizing / tuning virtual machines that are running windows 2003 / 2008 / 2008R2? There are some specific things I do but I can't find any solid documentation to compare to the measures I take. Thanks.
This will point you at the proper resources - http://partnerweb.vmware.com/GOSIG/home.html
Now this is a very "global" question and there's a much you can do to optimize guests. This starts with the proper virtual disk/partition alignment and NTFS cluster size and may end with deactivating e.g. the search service, etc. If you are looking for specific best practices applications (e.g. SQL, Exchange), Microsoft has some best practice guides for this in Technet.
Can you please specify what you are looking for.
What I'm looking for are settings that you would configure for every machine by default when you build it. For instance disk alignment, disabling the windows scheduled task for defrag on a 2008 machine so that all your 2008 machines don't defrag at the same time, etc. A guide for steps you would take for every virtual machine you build. Thats a generalization as you there will always be exeptions, but most machines you would want the settings applied to. A good example is the Windows 7 Optimization Guide For Desktop Virtualization from Citrix - https://support.citrix.com/article/CTX127050 which gives you good ideas on how to setup a Windows 7 machine optimally for VDI. I'm not concerned with the fine tuning for applications lik Exchange or SQL. Thanks for the comments.