I have Windows Server 2012 for my server right now, but I'm finding that everything I use on it has to be setup in Hyper-V with Ubuntu Server. Is setting up multiple virtual machines going to be efficient on my hardware, or am I better off just installing Ubuntu completely? I can't think of anything I would miss at all about Windows Server, besides the desktop enviroment which I can get with Ubuntu's Desktop.
I switched to linux from windows server a while ago and I'll never go back. But virtualising shouldn't be much slower than running it natively. I run a bunch of VMs on my server and there's no noticeable loss of performance.
Prefix Note: So I kinda went on a tangent about virtualising crap because of security. But basically switch to Ubuntu, if the server is has web facing applications (web server for example) virtualise them. If you plan to virtualise within Ubuntu consider switching to a type 1 Hyper visor.
The problem with servers when running a lot of services is security, especially if they are web facing.
Basically it can be though of as an umbrella; with no services running your umbrella is intact and no water shall pass through. For every service you start, you punch a hole into the umbrella, with which water can now get in through. So the more holes there are, the more likely the thing/person under the umbrella is to get wet.
Running multiple VMs is great for security, as you can have a dedicated machine for each task. The downside is the additional performance overhead and the additional load of managing more machines.
If the machine is not web facing and has no external access to it. You can just use a single OS and run everything within one.
As for switching to Ubuntu Server from Windows, you could as easily virtualise within Ubuntu and have a higher potential number of VMs you could run as Ubuntu (Linux in general) uses far less system resources leaving more available.
Instead of switching to Ubuntu you could consider moving to a Type 1 (Bare Metal) Hypervisor and installing all you need within that. This would be the best option if you plan to virtualise even after moving to Ubuntu.
Move from hyper-v to VMWare ESXI then virtualize.