Genymotion proposes a shell: the Genymotion Shell. It is not currently possible to start a VM with it.
But you can however launch a Genymotion VM thanks to this command:
player --vm-name <VM id | VM name>
This command launches the Genymotion’s player that gives you access to all the Genymotion enhancements widgets (GPS, battery, rotation, …), the screen scaling, rendering, … Like the standard GUI launch.
If you want to use a Genymotion VM without the enhancements, you can launch it via the VirtualBox command line like this:
VBoxManage startvm gui <VM id | VM name>
The VM id can be found thanks to this command line:
VBoxManage list vms
It displays a list of your VirtualBox machines on this format: name {id}.
UPDATE
Since Genymotion 2.5.0 you can manage all your Genymotion devices thanks to a command line tool. With this tool you can create, start, stop, delete, push files, flash the device, …
Here is a simple example to create a device and start it:
gmtool admin create "Google Nexus 5 - 4.4.4 - API 19 - 1080x1920" myNexus
gmtool admin start myNexus
This feature is available for paid licenses.