Skeletron. I enjoyed the overall design, particularly the Dungeon Guardian variant if you try to break in to his house outside his parameters. Plus, it is easy for my mind to drift to possible back story to the origins of the Skeletron, given much of the shadow magic and necromancy within the dungeon. It's simply a fascinating boss mob.
I love bosses like queen bee because the battle makes you stay on your toes and I also like the eater of worlds because of how much gore is spilled everywhere but I have to go with skeletron he is just so nostalgic at least for me and his reward is a whole dungeon full of goodies no other boss gives you so much stuff in return for beating him.
I'd have to say that for me, it's Queen Bee. Why? Well you get the Witch Doctor and the first set of Summoner Armor (If you decide to grind.) both of which are epic. And the fight in and of itself is great. The feeling and the atmosphere whenever you get into your first Bee Hive, and then break the larvae, yes, just... yes.
Eye of Cthulu - I remember when my friend and I were first playing terraria and we killed the eye. It must've taken a solid 5-10 minutes as we were using pretty much flails and bows. We started getting so scared we'd both die and my friend started squealing. His mum came in his room to see if all was okay.
The Calculus Brain of Cthulhu Jobs.
Jokes aside, it's the only pre-hardmode boss that actually FEELS like it has two phases. Skeletron is just a "parts" boss, and the Eye of Cthulhu uses the exact same tactics as the first phase, except without the minions and he does more damage. The Brain is untouchable until you kill all of it's minions, then you can begin phase 2 and actually fight it itself.
Something to add, it's counter part the Eater of Worlds also has interesting aspects to it, such as the fact that it is segmented and each of it's parts has a set amount of health. It's unique in that it can break apart and become multiple eaters if you make the mistake of breaking it up into different segments. Overall it's quite comparable in this sense.
I'm going with the Eater because it can be a really cool fight. Sure, it's pretty easy to cheese or tank but it burrows around out of sight and then strikes and if you split it up, it can be a very reactive fight because you're never sure where the next attack is coming from. It's at its best in an underground arena with a low level character (where you need to dodge and it can come from above you) but I guess there's never a real reason to fight it that way. Shame.