I recently did a clean install of macOS Sierra onto a 500gb hdd, and the only menubar/always running apps are Finder, Little Snitch (v3.8), Launchbar, Macs Fan Control, Endurance, Airparrot 2, and Tunnelblick. This is one of 2 drives in my mid-2012 MacBook Pro, the other being a 1tb ssd with known slowness and crashing problems .
Due to the 500gb hdd having similar problems as my ssd, I think that the issue may be hardware (maybe the ram?).
Also possibly related to hardware issues, every once in a while when I boot my computer (from a shut down state), the screen stays black even after booting up (I know because the keyboard lights up). The only way to make the screen work again it to reset my NVRAM/PRAM
Option + Control + P + R
I haven't tried exchanging the 2 8gb ram chips with others, but will do that soon to see if it makes a difference.