I am starting a new environment from scratch running two servers with Windows Hyper-V Server 2012 R2 installed. From there each server will run 2 instances of Windows Server 2012 R2 standard (DNS, AD, File Sharing) and some linux VM's.
For the Hyper-V hosts themselves, do you typically leave the domain as Workgroup or join them to AD once your guest VM's have AD configured?
Put the hosts on the domain. Otherwise management of them is more painful tham it needs to be. Its also a requirement if you ever want to cluster the two hosts.
However, since all your domain controllers are on there, if hyperv breaks badly you may have trouble logging in to fix it, if your cached credentials aren't valid.
Simple solution is to also have a local administrator account on each host - which you only use if your normal domain accounts can't log in. From that account you can fix hyperv and start the domain controller VMs if needed.
One other word of advice if all your domain controllers are virtual - do some research on how time syncing works. By default one of your domain controllers will be the time source for the entire domain. But virtual machines are terrible at keeping time. There are a few ways you can fix that, so do some research into it before everyobe complains all the computer clocks are 20 minutes slow.
Domain membership is recommended for servers running Hyper-V by Microsoft but then here is a quote from Microsoft technet blog:
Be careful when you are adding the Virtual Server host as a member of the same domain as the guest DCs it’s hosting as you may run into a Chicken & Egg problem if a DC is not available during boot time for the host.
Of course you can bring the HyperV Host into the domain but there are valid different opinions about it.
If all your Domain Controllers are virtualized, many believes, its not a good idea to bring the Hyper V host into domain. Well, surely you will be missing the advantages of having the HyperV host in the domain. And if you must, then you should consider having one physical server as domain controller or redundant dc guests on seperate hosts. There are lots of discussions available on this topic in the net. Here are a few links: Host Active Directory in a VM and have Hyper-V server a member of the domain
http://www.altaro.com/hyper-v/demystifying-virtualized-domain-controllers-part-1-myths/
https://community.spiceworks.com/topic/328774-domain-joined-hyper-v-server-2012-chicken-egg
