If you're just asking if you should have a "system" partition and a separate "application" partition, I don't see the value in it, especially now.
It used to be convention to do this for UNIX type systems because if the system volume overflowed with data, you could have situations that render it unbootable or unusable, so the separation of partitions was kind of a pseudo-physical way of preventing, say, unattended logfiles from filling up your boot partition.
Today you shouldn't see much benefit from it if you're properly maintaining systems. You could actually have issues now that updates are huge and system upgrades are so large; what was once okay in a 10 gig Windows install partition is now tiny. I've also seen issues because of the way Windows transfers files over the network and as temporary downloads where it fills the system partition and can't copy things over where they belong later, and it increased fragmentation problems on the filesystem horrendously.
If you're virtualizing this system then you won't even argue that you're getting better performance since the virtual machine is abstracted away from the physical disk layer, regardless of how many partitions/drives the VM thinks it has.
If your application is time sensitive to the point where you can't take the system down for a disk check (hopefully you'd rarely ever need it), you should probably have plans in place that you have failover support, maintenance windows, and in the case of the VM, you could probably have a way to keep the VM running while diagnosing an issue with a snapshot or copy in a sandbox if need be. If the operation is critical, you should already have plans in place to keep the service available if the machine were to fail. That builds in the ability to fix the virtual box without interrupting service. Otherwise, your users will have to live with a period of downtime.
Also, Windows is finally gaining more flexibility (and Linux already had this) in creating on-the-fly volume management that can grow and shrink drives and combine them into larger volumes (like Linux LVM support). Windows is slowly moving away from the drive-centric model and more into the volume management model on servers.
The services you mention already have some redundancy built in if you're using Windows DC's, so time for a chkdsk should not be an issue for many of them.
Overall, unless you have a direct need to create a separate volumes as drive letters I'd create one large drive and leave it at that. It's simpler, it's more flexible down the road, and it's overall a smaller PITA to deal with.