The best boss fights in Skyrim I've mostly had because of mods.
There are two, nobody will read them but yeah I thought they were cool.
1: Fight against Alduin. Something clearly malfunctioned with my deadly dragons mod, because in the final area there were, at all times, at least four or five dragons swooping me and fighting. So when I made it to the keep and got the other heroes, it was like we were actually fighting in a dragon war. When we were outside it took like 40 minutes to actually use our shouts together without getting swarmed by dragons.
During the Alduin fight there were still dragons everywhere that the npcs were doing shit against. I'm not even sure how it happened because nobody I've spoken with that has deadly dragons mod has had this happen to them. I was amazed after having that much fun, that it wasn't in the vanilla game.
2: This one is less of a boss fight and more of an embarrassment but I thought I'd share anyway. On a new playthrough I was just exploring the world, hadn't even unlocked dragons yet. To my surprise north of Solitude I saw what looked like a Dragon flying through the air so I went to investigate. It looked like a normal dragon, so I thought I'd just kill it. Big Mistake. As soon as I shot at it, there was a noise like thunder cracking, and meteors fell from the sky, and I saw that my arrow hadn't even budged its healthbar. I found it impossible to kill because whenever I'd ready an arrow I'd have to sheathe it to dodge a meteor, and the swooping knocked me off my feat a lot. Had to make a strategic retreat, but it was very fun.