Most energy efficient computer

AM1

We'll start out by saying what you need to actually do the work:
- Quad-core or better CPU since you are running two VMs and an XBMC frontend.
- The CPU needs to have virtualization extensions (VT/AMD-V) to run VMs very effectively.
- Video decode hardware or CPU cores fast enough to play back 1080p video. Software decode is the easiest to deal with as it always works if you have a fast enough CPU- all you are doing with the graphics is outputting video over Xv which is essentially foolproof. Trying to get decode acceleration from your GPU through XvBA/VDPAU/VA-API is a much more hit and miss affair. My personal experience shows that 1080p H.264 at 40 Mbps Blu-Ray bitrates (ugliest stuff you should see on an HTPC at the moment) requires a ~3.0 GHz or better Core 2 Duo/mid-2 GHz or better Haswell Core i3 or something with >4 cores if you have the multithreaded ffmpeg H.264 decode in your distribution.
- Enough RAM to allow everything to work, particularly your VMs. It sounds like you want 16 GB at a minimum as running Windows is an 8 GB+ affair, and then you need some left over for the Linux VM, the bare-metal Linux OS, and XBMC.
- Enough disk space to run everything
- You said frontend for XBMC, so I assume the video capture and storage is elsewhere. You'd need to have a video capture card or two in this machine and sufficient PCIe slots to run that if you have a self-contained XBMC machine.

You have a few different ways to go here.
1. AMD Athlon 5350. This is a 2.05 GHz 25-watt quad-core Socket AM1 APU with AMD-V and can support up to 16 GB of RAM at the present time. The APU supports XvBA so you should be able to get video decode assist. This isn't going to be terribly fast for running VMs and I wouldn't guarantee that you can do software video decode either.

2. AMD A10-7700 or -7850K. These are 95 watt quad-core FM2+ APUs with AMD-V and clock speeds close to 4.0 GHz. They'd have plenty of power for your tasks but at stock speeds are 95 watt chips. Fortunately TDPs are configurable and you can use a tool like TurionPowerControl or perhaps your board's BIOS to crank down the maximum allowable wattage, voltages, and clock speeds to result in a pretty speedy, low-power chip. I use TurionPowerControl to adjust voltages and p-state transitions on my Bulldozer Opteron and it's a really handy tool.

3. Intel Core i5s that end with a "T." These are 35-45 watt quad-core LGA1150 chips that have Turbo Boost and VT. These will be 2-5 times as expensive as the AMD chips unfortunately.

4. Intel Xeon E3-1230L v3 or 1240L v3. These are essentally 25 watt versions of the above i5s but cost even more.

I'd personally go with the A10 based setup as that would give you the most bang for your buck, should be enough grunt to do what you need to do, and you can always "turn up the juice" later adn return the CPU to its full 95-watt TDP performance level if you need to. The Intel units would be much more expensive but would work well for this usage case as well, plus they'd be low TDP right out of the box with no work required. I'd get a micro-ATX motherboard unless you are for sure only going to be using this machine as a "dumb terminal" for XBMC as the mini-ITX stuff generally only has one PCIe slot.

Usually running an operating system natively is more energy efficient than running it via VM.

If I had his scenario, I'd just buy a Surface 3 tablet.
It runs windows, and Linux. An x86 based atom processor powers the thing.

Linux can be ran from a Raspberry pie as well.