For me it's a tie between two, neither of whom have appeared on this thread. (EDIT: Or they were when I started typing this half an hour ago, but it appears Lotuseater hates one too, but for different reasons).
The first is Arondil of Yngvild Barrow. Why has a boss in one remote dungeon earned a place earned a place on my most hated NPC list? Because I never recovered from reading his journals detailing his lust for the milkmaids of Dawnstar sliding into full blown necrophilia then watching him catch sight of my female PC and saying: "Ah! Another plaything for my collection!" Luckily I am able to kill him with zero consequences or moral qualms. I relish killing him. But whenever I roleplay characters who don't have any reason to go near Yngvild, it's hard to stay away. Real hard.
The second I might cope a bit of flak for and will make people hate me, but it's Brynjolf. I really object to the way he decides based off the way I dress and act that I am a thief. My first character had earned every single septim of her money honestly, so I was very annoyed when this red headed creep marched up assuming that not only was I a thief, I'd be totally happy to help him with his dishonest plot to frame an innocent shopkeeper I'd already spoken to and liked WAY better than this dick who thinks I don't walk and dress as befits my station and morality.
If it was just that, Brynjolf would only be on my: "Jerks in Skyrim" List with the likes of Nazeem, Heimskr and Braith. What elevates him to the list of most annoying NPC is the man is completely incapable of taking a hint. If you don't feel like going through Brynjolf's entire long conversation when he first approaches you, you can tab out. If you this, Brynjolf will say: "I can take a hint lass. Come find me if you change your mind." This is the biggest lie a Skyrim NPC has ever told me. Every time I get into a two foot radius of Brynjolf for the rest of eternity he says: "Glad to see you came to your senses lass. Ready to make some coin?" Brynjolf, I wasn't ready to make some coin the last 98648224 times I went near you, so why the hell do you think 98648225th time is going to be different? Take a bloody hint!
After playing one character who lived in Riften and wasn't a thief, the only thing which stopped me from killing Brynjolf was his essential status. One time I decided to say yes and do nothing to see what happened. After he finished his scripted distraction he just stood there silently for five minutes grinning and pointing at his Elixir until I got bored and reloaded, but I saw a Let's Play where the guy wandered into the Ratway and Brynjolf yelled at him and made him try again. So when my current character goes back to Riften I'm going to keep doing that and see if Brynjolf eventually snaps and refuses to let me in the Thieves Guild or if he keeps giving me chance after chance after chance.