So, after installing PulseAudio Equalizer and Lollypop and yes, tweaking the Pulse's config file a bit with not much knowledge, I have lost my audio after a reboot. Output devices have disappeared, Ubuntu is on permanent mute, I have no idea what to do. Help!

System: 16.04 LTS
Laptop: Thinkpad 64-bit
Processor: Intel® Core™ i5-4210M CPU @ 2.60GHz × 4

Try installing pavucontrol and see what that reckons you have and what is enabled. Pity you didn't keep a copy of the pulse config file but you may find that you have one user local rather than system wide so depends which one you changed.

I installed the pulse equaliser and didn't touch anything else and it just worked.

One desperate option if Ubuntu has the facility is to uninstall with a clean up and install the lot again. You can check that the kernel is spotting it correctly by looking at the boot up log. As I understand it that indicates that the nuts and bolts of alsa are ok - pulse links into that and it's equaliser takes the output from that. Pavucontrol is often a good idea if pulse is about.

John
-