To clear this up before I start, what defines a boss for me is three things ;
•Uniquely named e.g Sigdis Gauldurson, Haknir Death-Brand etc. •You can tell if it is a boss if your quest has an objective to kill a specific person ; if this person is named, it is a boss
Now, to start :
I've encountered alot of enemies in Skyrim. As a Level 61 Mage, I have done around 90% of all quests in the game. There are no side quests left for me anymore. I have completed the Civil War line of quests, the Daedric artifact line of quests, the main questline, the Thieves Guild questline, the Dawnguard questline, the Dragonborn questline etc. The only reason I continue is that I want to one day face the Ebony Warrior at Level 81.
And through my travels throughout Skyrim, these are the hardest boss fights I have came across.
1) Miraak, the first Dragonborn - The final boss of the Dragonborn DLC is by far my hardest opponent I have yet faced. I tell you now, the lightning spells he uses will deplete your health as if you were a Horker waiting for its inevitable slaughter. I came prepared with 30 health potions, a very large amount of them strong health potions too. I came out of Apocrypha with one Ultimate Healing potion...
I have an enchanted Daedric Sword, which so far has easily let me slay any foe. I admit, it did some decent damage to Miraak. But his lightning spells just made my health go down in literally a half of a second. I subsequently died when trying to melee fight him.
Then I tried to use magic on him. I conjured Daedra, Mistmen, used fire storm against him! All to no avail. And don't even get me started on his shouts...
The fact that he can make a proud Dragonborn like me cower in fear behind Mora's stacks of books is enough to make him my #1 hardest boss fight. To note : I eventually defeated Miraak after 30 minutes of cowering behind book shelves.
Not a quest "Boss" but definitely boss caliber; Naaslaarum and Voslaarum. Had to reload so many times fighting these guys. --- I do so love Riften. I journeyed here in my youth. A thief took my purse... so I took his eyes. It was a fair exchange.
Miraak was a b****. The Ebony Warrior? Best fight of any TES game I've ever played. That s*** was awesome. Trading blows on a snowy mountaintop with someone who can actually hold their own against me... I wish he would respawn.
Karstaag was hard, too, but I was kiting him the whole time to avoid that stupid Frost cloak and his Blizzard. The EW was a much more entertaining battle. --- Hey there, sweetroll; I just cast Oakflesh... if you know what I mean.
As my primary mage character? None. Endlessly staggering enemies is hilariously op, even more so with a 0 cost Ignite. As my warrior? Probably Karstaag. Freaking insane. And he turned my dog into a ghost. --- Life is a concert, and I'll be your closing act.