Brilliant, but Lazy: Tatl has almost encyclopedic knowledge of the monsters, people, and history of Termina, seems to have photographic memory when it comes to maps, and knows a fair bit about magic. The Great Fairy of Clocktown believes that if Tatl had kept to her studies, she could have been "capital 'G' great", as Tatl puts it. Even so, she'd rather be pulling pranks with her friends.
Clingy Macguffin: Of course, there is the Deku Mask during the first arc, just like in the game. Additionally, from a literal standpoint, Link notices that the Ocarina and any Masks he gets have a strange tendency to cling to his belt no matter how much running and fighting he does.
Darker and Edgier: Yes, even moreso than Majora's Mask was to begin with. The Song of Time only works for five loops, counting the one Link spends trapped as a Deku Shrub, so the race against time is even more pronounced here than it is in the game. What's more, the scars Link carries from his adventures in OoT play a major role in his character, and he and Tatl spend more time bickering than helping each other for quite a few chapters.
Link seems to think that aspect (among others) is rubbing off onto him... and he's not very happy about it.
Face Death with Dignity: Mutoh and Viscen opt not to flee Clock Town, and spend the last six hours drinking together.
Fantastic Racism: The Deku Scrub king is prejudiced against monkeys and humans, and probably anything else that isn't a Scrub. Tatl also seems to dislike the healing-type Fairies.
Genre Savvy: When Link gets the bow in the temple and realizes he doesn't have any arrows, he goes all the way back to Clock Town to find some because he knows from experience he will need them to deal with whatever is at the heart of the temple.
"Groundhog Day" Loop: Averted. Unlike the game, Link and Tatl are physically traveling back in time instead of resetting it.
Heroic Mime: Link, during the first few chapters. Justified though, because he cannot figure out how to talk as a Deku.
Heroic Sacrifice: Tatl explains that healing-type Fairies give up their life energy when they heal Link or other adventurers, but she considers this a Stupid Sacrifice on their part and doesn't think much of them.
Hive Mind: The author's explanation for why the Great Fairies become split into multiple smaller fairies.
Lightning Bruiser: Odolwa, which makes Link's victory over him all the more impressive.
Loyal Phlebotinum: The Ocarina, which does nothing for Skull Kid, will actually change into entirely different instruments so that Link can play it regardless of his body.
Madness Mantra: One of the Gorons. "It's so cold out there and so loud in here and so cold out there and so loud in here. It's so cold out there and so loud in here and so cold out there and so loud in here and..."
The Mafia: Jim, leader of the Bombers, runs the group like a mob boss.
Mysterious Past: The audience knows Link's past. Tatl however, does not, and she becomes hellbent on finding out the longer she travels with him. That Link refuses to speak about it only makes her more curious.
Though in recent chapters, Link has progressed from "I don't want to talk about it", to "Maybe later", and finally to "Sure, why not".
Shell-Shocked Veteran: Link again, complete with grouchy stoicism and flashbacks. Most of his character development involves him moving out of this mindset.
Suddenly Voiced: Used as a Meta-joke when Link first opens his mouth after getting the Deku curse removed.
Stable Time Loop: At the end of the first cycle, it is revealed that instead of following the game's Reset Button version of time travel, there are instead five versions of Link and Tatl running around different parts of Termina at the same time.
What the Hell, Hero?: Tatl lectures Link on the double standard of him being unwilling to kill Guays that were trying to eat her, when he was willing to kill a Skulltula that was trying to eat him earlier on.
Why Did It Have To Be Birds?: Tatl is cripplingly frightened of birds, which makes sense, since they're faster than her and can easily eat her.
Link has a similar dislike for Deku Babas, the first enemies he fought.
Wise Beyond Their Years: Link, of course. His overall demeanor is that of a warrior who's seen too many battles, which is at odds with his ten year old appearance. However, as Tatl explains after Link asks if he's "Odd":
Tatl: Link, you're weird for all kinds of reasons. You fight giant monsters like it's just another day's work. You move with that sword and aim that bow like the hero of some kind of folk tale, the kind where the hero wins, and you're not even old enough to have facial hair. When we met, you were casually strolling around the forest with a little blue thing that changes the flow of time, and you just left it sitting on your belt for any old mugger to take... You have clearly handled explosives before because I haven't even seen grown carpenters use bombs without wetting themselves a little bit. You're all kinds of insane, you're one giant boy-shaped ball of contradiction; I don't even think there's such thing as a boy-shaped ball; and you know way too much about time travel for anyone under the age of one thousand. So, uh, the fact that you seem a little more calm than you ought to sometimes? That's not really a standout.
Year Outside, Hour Inside: The Underforest, which Tatl, Tael, the Skullkid, and Link used to travel between Hyrule and Termina. While probably only a few hours behind the Skullkid and Tael, Link and Tatl arrive in Clock Town a few weeks after them.