I have the exact same symptoms on my mid-2012 MBP (nVidia + Intel) running 10.11.6. I do software development in a bunch of VMs every day, and this definitely started in the past couple weeks. I think it's likely a bug or incompatibility between the latest OS update and VirtualBox.
None of my guests use 3D, so I've rolled back from VirtualBox 5.1.12 to 5.1.10 to see if it makes a difference. The VM that seems to be the trigger does use the guest additions, though, so there's some interaction on the video side.
I'm leaning towards an OS issue (perhaps a new video driver) on this one, because even after shutting down the offending VM, followed by all the others (an awful experience with the constant hangs), I still get really laggy scrolling or resizing in a browser window and end up rebooting.
Here are some of the logs, lots of video detaching and watchdogs:
Dec 29 10:09:29 myhost kernel[0]: stalling for detach from IntelAccelerator
Dec 29 10:10:14 --- last message repeated 1 time ---
Dec 29 10:10:23 myhost kernel[0]: stalling for detach from IntelAccelerator
Dec 29 10:10:38 myhost kernel[0]: stalling for detach from IntelAccelerator
Dec 29 10:10:38 myhost kernel[0]: stalling for detach from nvAccelerator
Dec 29 10:10:49 myhost watchdogd[353]: [watchdog_daemon] @(_wd_daemon_service_thread) -
service (com.apple.WindowServer) reported as unresponsive
Dec 29 10:10:51 myhost spindump[683]: Saved userspace_watchdog_timeout.spin report for
WindowServer version ??? (???) to /Library/Logs/DiagnosticReports/WindowServer_2016-1
2-29-101051_myhost.userspace_watchdog_timeout.spin
Dec 29 10:10:51 myhost spindump[683]: Removing excessive log: file:///Library/Logs/Diag
nosticReports/WindowServer_2016-12-22-104433_myhost.userspace_watchdog_timeout.s pin
Dec 29 10:10:51 myhost watchdogd[353]: [watchdog_daemon] @(__wd_service_report_unrespon
sive_block_invoke) - spindump gathered for (com.apple.WindowServer) at (/Library/Logs
/DiagnosticReports/WindowServer_2016-12-29-101051_myhost.userspace_watchdog_time out.spi
n)
Dec 29 10:10:53 myhost kernel[0]: stalling for detach from nvAccelerator
Dec 29 10:11:14 --- last message repeated 1 time ---