I’ll give this one to the first Mother Brain. That realization that she was in control of the planet you were fighting through the whole time. She never attacked you directly. 

Such epic ness getting past the first Metroids and pounding her face like a red door. 

The fight against Mother Brain is Metroid 1 is so annoying with all those shots coming from everywhere and the knockback from getting damaged pushing you into the lava. 

Yeah Ridley and the titular final boss both from Metroid Prime top the list for me too.

Both of them epic, challenging, and a great test of all the skills and abilities you've built up to that point. Putting them down feels truly well earned.

And yeah, the freefall fight with Ridley in Prime 3 is awesome as well.

I know it tested my calm lol

I would add Diggernaut (Samus Returns), Rundas (Prime 3), Phantoon (Other M), Ruins Test (Zero Mission) and the Security Robot (Fusion). All of these are very good boss battles either for their mechanics, challenge or story impact.

I'd say not just the best Metroid boss, but one of the greatest boss battles of all time.

Lots of great answers so far. I'm going to pick Draygon from Super Metroid.

That monster is super scary and dangerous, very hard to beat and a real challenge. But once you managed to beat it something unique hapens: mini-Draygons come to the dead body and drag it down into the sand. When I saw this for the first time I realized that I killed a mother and the children came mourning, and that was very strange because on the one hand I felt relieved for finally beating the fucker after a hard battle but on the other hand I somehow felt sorry and sad at the same time.

Did you know that there are two ways to defeat Draygon? Usually you beat it by shooting at his belly when it swoops down on you, but there is a hidden method as well, a very cruel and gruesome method, by frying it with electricity. It's much faster but it terrified me.