Wow, tough question,
My least favorite:
Agitha: Ok, Agitha just creeps me out. She's this little girl who lives by herself in a bug infested creaky old house that is not up to safety standards at all. Like seriously, bugs are nasty and half of them will kill you if you touch them!
Agitha: "Wait here Link, I'm going to show you my favorite bug!"
Link: *Awkwardly leans against a wall*
Enraged Bug: *Bites Link six times on the forearm*
Link: *Dies*
Agitha: *comes back* "Here it is Link! The- um- oh my..."
Ingo: first of all, in case you didn't know, Ingo and Talon are a not so subtle allusion to Mario and Luigi. And while I liked Talon, Ingo was just a huge jerk! In Oot, he sells out poor Talon and Malon. And for what? Ownership of Lon-Lon Ranch and servitude to the Dark Lord Ganondorf. Jeez, what a jerk! To make it worse, in MM there are three of them that were trying to steal the milk from Cremia. (Btw that is probably my favorite side quest ever!)
Now for my favorite characters (not necessarily in order):
Link: I know this might not seem like a very original choice but he is one of my favorites! He has really been one of my role models. I look at him in the beginning of Twilight Princess, even on his day off he plays with the children of the village and helps the people who are in need. But if you think he's just some perfect hero, look again! After he gets the master sword in Hyrule Warriors, he gets cocky and many people get hurt because of it. So Link is definetly one of my favorites.
Ravio: I just love this character! He's so different from anyone else in the Zelda Universe. When he first is introduced, he kind of takes over your house and makes you buy his overpriced items. To make it worse, when you die, he sends his bird friend to pick through your remains and take the items back. But in the end, he turns out to be the Lorule version of Link. He even has the sick purple hair!
The Happy Mask Salesman:
The Happy Mask Salesman is a seriously trippy character. No one knows who he is, where he comes from, or anything about him in general. Why does he carry the Majora's Mask around and how did he find it? Also, how is the only one who knows that Link is not from termina? I think that the Mask Salesman is so wierd that you can't help but love him!
Tatl: In MM, Link's companion is Tatl. She starts off pretty rough towards Link but she warms up to him in the end. In the end of the game, you can see the relationship between Link and Tatl when they are talking about stubborn people and Tatl says: "That sounds like someone else I know!" So you can see how through this playful banter that hey have a cool relationship.
And many more...
You may have noticed that I really like the characters in MM. This is because (this is true for at least clock town) every single character has a deep backstory that has been well thought out and planned. (Cudos to Nintendo on that) their stories often intertwine with others too. This is one of the reasons why MM gives you such a magical feeling. And also why it is, in my opinion, one of the greatest games ever.