Recette, from Recettear: An Item Shop's Tale, could only accomplish what she did because she was so lovable. It's even lampshaded in the dialogue. "That girl: something about her inspires people to care."
Tielle, the young elf, is just as moe. Whereas other adventurers have a special business card, Tielle's is a picture of her and Recette together. The item description is 'Adorable beyond words.'
P4 also contains a fairly hilarious subversion using a character from P3, to boot: Chihiro, of all people, shows up during the school trip to Iwatodai, as the class president of Gekkoukan High. She isn't "moe" anymore (her fear of men, ah, having been conquered). Instead? She's now only about a half-step under Tina Fey in terms of straight-out hotness.
On the topic of Persona, P2's Jun Kurosu. Jesus Christ, just, Jun Kurosu. Even his first demon contact is called "Moe Face". Then there's the one involving Ginko putting Jun in drag and him looking so cute that the female demons adore him and the male demons are scared of him. Hell his official profile talent (amongst fortune telling and flower language) is CROSS DRESSING. Oh Atlus.
From BlazBlue, we have Noel Vermillion, an adorably ditzy Lieutenant for the world government who, whenever you see her, you'll just want to give her a big ol' hug! Provided you're not a member of her Hatedom.
Tsubaki might be inching in this direction if she keeps getting mind raped the way she is, too. Though to a lesser extent than Noel.
Fire Emblem loves this, especially if they initially appear as enemies, as their faces scream "recruit me" because tons of them are just innocent girls dragged into battles by villains.
Ilyana from the ninth and tenth Fire Emblem games is not only incredibly cute, but has an absolutely insatiable hunger. Several of the characters have reported her using her cute face and vulnerable appearance to swipe unsuspecting men's food.
FE 7 has Shrinking Violet Florina and Plucky Girl Nino, FE 4 has Rana, Yuria and Tinny; FE 8 has Myrrh, Neimi and Amelia and the third game has Tiki, Maria and Yumina. Thany from FE 6 is a subversion; she has a moe face, but timid and vulnerable are not in this girl's vocabulary. Fa and Sophia, on the other hand...
And in No More Heroes 2: Desperate Struggle, Shinobu says "moe!" on receiving items and will taunt enemies with "you've got no moe!" She also asks "what does moe mean, anyway?" while saving.
There's also Pure White Lover Bizarre Jelly, the offensively moe Cliché Storm anime that Travis watches in both games. It needs to be seen to be believed, and it can make you feel creepy even if you're asexual and a girl.
Horribly enough, the reason the moe-figures work is because the male characters have surprisingly moe personalities. Snake alone is a aloof/warm-type TsundereIll Girl who makes nonsense vocalisations, is devoted to his best friend, and gets a lot of Panty Shots. Otacon is so moe it hurts.
And the kicker is Raiden, designed as the beautiful bishounen, is * not* moe. It's his personality, and specifically the examination of his selfishness and abusiveness at the end of MGS2 - it's impossible to go "aww" after that. But the legendary mercenary and his "best friend"? Awww!
Emma from Metal Gear Solid 2 also qualifies.
Mei Ling is also quite cute, and her Tsundere moments (like her Easter Egg appearance over the codec in MGS 2) make her even more so.
Paz from Peace Walker. Large anime eyes, schoolgirl outfit, cute gestures and features, optimistic personality. Which serves to hide the fact she's actually an asshole double agent.
The meme of Yuka being called "youkai moe" is actually from Word of God, but it also should be mentioned that Yuka is a flower youkai, and the literal meaning of moe is budding or sprouting (ie as a flower). Therefore, Yuka is less of an example and more of a victim of an Incredibly Lame Pun most English speakers won't get.
Make way for Kogasa, the new Youkai Moe~. How can you say no to a face like this? It's even stated in canon.
Chen (also known as CHEEEEEEEN!!) is also a notable example, existing mostly to be as adorable as possible.
Koishi Komeiji is often portrayed in the fandom as being a lovable Cheerful Child, and while her appearance can give off this vibe, her actual back-story makes her more of The Woobie.
Hata-no-Kokoro, is sometimes treated as one in fandom, for being fairly young by Yokai standards.
Nakoruru and Rimururu of the Samurai Shodown series are very much siblings made of pure concentrated moe. Nakoruru moreso, as she somehow got herself recognition as one of Japan's most moe characters.
Interesting fact is that when Samurai Shodown received an OVA, Nakoruru gets to be voiced by the actress who played Mei, as listed in the Live Action TV section above. So that means what's already moe, is dialed Up to Eleven.
There's also Estelle from Tales of Vesperia, full of so much Moe to go hand-in-hand with her Damsel in Distress role. In addition, she's adorably naive and gentle, though it wears off to a degree as the game progresses. She does start off as a girl who wants to make graves for every monster she kills.
Disgaea 4 introduces Desco, the Cute Monster Girl / Eldritch Abomination, who's easily the most moe character in the series to date. She's got a Verbal Tic, refers to her teammate Fuka as her "onee-sama", speaks in the third person, and generally ends up coming across as innocent and/or a goofball whenever she says anything, even when making death threats.
Space Invaders Extreme 2 Stage 5-D has, in the background, a cute girl dressed in an alien-like costume.
Liara T'Soni of Mass Effect. Tali'Zorah nar Raaya is equally cute, but much snarkier and less of an innocent.
Though if you romance Tali as a male Shepard in Mass Effect 2, she gets so adorably flustered you can practically FEEL a Luminescent Blush coming through her faceplate.
In Mass Effect 2, a conversation between a Quarian girl and a Turian implies that Quarians in general instill this sort of reaction in humans ("It's always the same with humans: 'She gets sick easily! She's so vulnerable! I wonder what she looks like under that helmet...'") This could be considered a Lampshade Hanging of the general fan adoration of Tali.
Legion. Yes, Legion, at least once he's opened up post his loyalty mission.
Princess Zelda from Spirit Tracks. Somehow manages to become cuter in the form of an ungodly metal golem of ghost armor four times her size.
Zelda's moe returns in full force in Skyward Sword. The brighter art style and the fact that she looks younger than her Twilight Princess incarnation probably help.
For that matter; Toon Link, Toon Link, TOON LINK. He makes every game he is in about ten times cuter. You really want to cuddle him whether it's for his many endearing facial expressions or his adorable little battle cries.
Moemon is a Game Mod of Pokémon which replaces all of the Pokemon sprites with moe gijinka.
There are varying versions of the moe sprites for different hacks. Some are meant to be female-specific, while others could easily be mistaken for men if not for the gender symbol. A couple are male-specific, sorta, but not many.
Ōkami: Origin of all that is good, and mother to us all, Amaterasu. AKA Ammy. AKA Fluffball. AKA Snowy, Fido, pooch, and Snowball. And Powderpuff. We all know she's a full blown deity reincarnated as a wolf, but dammit if she ain't the cutest thing in the world when she's wagging her tail.
Ōkamiden sees your puny example and laughs derisively at it. Then you look at this◊ and say "D'AWWWWWWWWWWWWW!"
Miyu from Trinity Universe. She's a talented Starving Artist who is supporting her family. She is shy and uncertain. She wears A-Rank Zettai Ryouiki. And she's a Cat Girl, complete with ears and tail.
Valkyria Chronicles resident Moe Isara Gunther is also the squads tank operator, making her and her Bishōnen brother the most powerful unit in the entire game.
Asha of Monster World IV is ridiculously cute. She was also the least popular character in the series, unfortunately, owing perhaps to the moe phenomenon not having arrived yet.
Athena Asamiya from The King of Fighters was always a fairly cute girl in all of her appearances but for the moe qualities, was usually outclassed by other characters (such as Kula, Yuri, or Momoko). However, by the twelfth installment, she was redesigned and fell squarely inside the definition.
Vivi from Final Fantasy IX is the best example in the series. He has many of the standard moe traits: he is clumsy, shy, young and innocent. Add in existential angst to justify his social awkwardness and a doll-like appearance and you have a character that most players just want to give a hug to.
Tifa from VII can get pretty Moe at times, especially when she acts so shy and awkward around Cloud.
Aerith is quite Moe as well.
Can't forget Yuna and Rikku from Final Fantasy X, especially with how Woobie they both are.
Isabella in Advance Wars: Days of Ruin. Possibly Penny as well, although it's offset by all the crazy.
Alistair in Dragon Age I. He is so innocent and shy, its adorable! Then he goes all knight in shining armor, or tries to, once you romance him a little.
When compared to food, one Dragon Age writer said Alistair is like "strawberries and cream, sweet and wholesome and delicious, and a little goofy." Another said he is like an apricot "Cute, sweet and just a little fuzzy."
Leliana is also terribly moe.
Bethany in Dragon Age II. The face system seems designed to give her moe eyes if you make a custom face.
The Maiden in Black from Demon's Souls; she is so cute that if you kill her, she will resurrect shortly after, and then apologize to you for not being able to die. The way she swings her feet on the stairs while waiting for you to get back is also nothing short of adorable.
Every female character from Panel de Pon qualifies in some way or another, but Lip especially.
Isabelle from the New Leaf incarnation of Animal Crossing definitely counts as one. Just ask Google Images.
Nearly every character design in the Hyperdimension Neptunia series is based on this to the point where one of the promos for the third game has a caption that just says "TONS AND TONS OF MOE!"
Low Chaos Corvo Attano, from Dishonored. At least the fandom thinks so. He just want to put Emily on the throne with the least blood shed, and he's utterly loyal to her and the conspiracy to crown her. And all his interactions with Emily are adorable. At the beginning of the game, Corvo can play hide and seek with Emily, and when she is first rescued, Corvo gives her his arm all the way back to the Hounds Pits. His unflinching loyalty to his dead Empress and Emily is utterly cute, even if he does eat rats.
Ratonhnhaké:ton/Connor Kenway from Assassin's Creed III. Murderer he may be but he's a big, awkward, sweet man who's naďve and coltish; and very cute for that.