Starting in june 2016, Docker can be run on Microsoft's Hyper-V virtualization on Windows 10 hosts. This is now the preferred and "official" way to run Docker on Windows.
https://docs.docker.com/engine/installation/windows/
Hyper-V is a Type-1-Hypervisor, meaning docker will run one layer closer to the host hardware and perform significantly faster than boot2docker (which uses VirtualBox, a Type-2-Hypervisor, running inside the host OS).
The performance benefit for docker has a downside too: Enabling Hyper-V will prevent hardware virtualization features for Type-2-Hypervisors, therefore existing VirtualBox images can not be used with VTx, and you might want to consider moving other virtualized OSes to Hyper-V as well.
Windows 7-8.1 hosts can still use boot2docker to run Docker containers, but the main development focus for Docker on Windows is the "new" Hyper-V-Docker.