Mac Mini mid 2011 (5,1) 2.3 GHz i5, 2 GB ram running 10.12.1 with 149/500 GB free.
In application monitor everything (memory, disk, network, cpu usage) is nominal.
Disk check (Cmd+R at boot) – Passed
Hardware test (opt+D at boot) – Passed.
On boot the screen goes white after 45 seconds (half of the boot loading bar) and the dock shows up after about 5 minutes. The top bar take lot longer.
Safe mode – still slow as molasses. 78 seconds to launch a new Finder window. Over 5 minutes for System Preferences. Over 5 more to launch any of said preferences (if they don't fail to open)
Already reset the SMC and PRAM. Turned off all spotlight indexing though that wouldn't affect safe mode. Nothing plugged in besides a keyboard, mouse, monitor and Ethernet cable. Tried single sticking each RAM module. Really banging my head against the wall here. Even ssh'ing in from another machine on the network is a drag. 'ls' of a directory with 12 files takes 4 seconds.
Oh and Console keeps crashing. Because of course.
Could anyone recommend a next step?
EDIT: output of vm_stat after a fresh boot into safe mode
Mach Virtual Memory Statistics: (page size of 4096 bytes)
Pages free: 3827.
Pages active: 103786.
Pages inactive: 100841.
Pages speculative: 3730.
Pages throttled: 0.
Pages wired down: 118363.
Pages purgeable: 0.
"Translation faults": 4213483.
Pages copy-on-write: 1353750.
Pages zero filled: 779909.
Pages reactivated: 566180.
Pages purged: 9028.
File-backed pages: 69729.
Anonymous pages: 138628.
Pages stored in compressor: 526296.
Pages occupied by compressor: 193246.
Decompressions: 310835.
Compressions: 1264824.
Pageins: 837784.
Pageouts: 1602.
Swapins: 2409.
Swapouts: 3813.
Best Answer
It sounds like a lot of the speed problems you're having comes from running newer software, macOS 10.12, that usually requires more system resources on a computer that has insufficient RAM (2 GB just does not cut it practically) and a slower HDD. However I don't think that would normally cause quite the amount of speed reduction as you have reported.
Nevertheless, for a quick speed boost, I would definitely recommend upgrading to 8 GB of RAM. Apple has information on how to upgrade, just make sure that the RAM you get is compatible with Apple's specifications. For example an 8 GB RAM kit from Crucial should work.
Additionally, I do know that HDDs can be a speed bottle neck, especially as they get more full and are older. You can upgrade to an SSD (here's a guide by Crucial), however that is a far more complicated process, and you will also need to transfer all your software from the old HDD.
But your speeds are very slow, so there is probably some software problem. You can try to diagnose that by going to System Preferences > Users & Groups > Login Items and see if you have programs loading at boot. Also if you can check Activity Monitor, that may show if something is using a lot of your CPU. In the end, you may need to do a backup, wipe your hard drive, reinstall macOS or an older version of OS X, and transfer your documents and settings.