All spoilers will be unmarked ahead. You Have Been Warned!

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Main installments:

Danganronpa: Trigger Happy Havoc

Makoto is small, humble, clumsy, and incredibly earnest. The fact that his darkest secret is that he wet the bed until he was in fifth grade, compared to such secrets as fratricide, only furthers his image as a dork.
If you can get past his loud voice and insistence on the rules, Kiyotaka is a huge dork who has no idea how to make friends.
There's something to like about Hifumi's Otaku obsessions. Unlike most examples, this isn't portrayed in the most flattering fashion.
Yasuhiro becomes dumber as the game goes on, and is hilarious whenever he thinks his predictions are spot-on.
Despite his conscious efforts to maintain a "cool, tough punk" persona, Leon has several shades of this. He gets endearingly enthusiastic and giddy if you pick the right choices in all social interactions with him, and he's revealed to be somebody who's incredibly self-conscious about looking cool. He even invokes this trope in one of his School Mode events, when he speculates that his inability to eat a burger without dripping everywhere may endear him to girls.

Danganronpa 2: Goodbye Despair

Chiaki, especially when she puffs up her cheeks to show she's angry like a child having a tantrum.
Sonia tends to get overexcited over the smallest things, and tries to look hip by using old school sayings like "Oh snap" and "Fo' sho"
Many fans agree that, in spite of his Evil Overlord persona, Gundham's Chuunibyou antics are quite adorable, especially when he gets genuinely flustered when complimented by Sonia. The interior of his cottage also implies that he reads bedtime stories to his "Dark Devas of Destruction", given that he has a rocking chair and numerous books by their cage.
Although she initially comes across as intense and distant and is a fierce warrior, Peko can actually be rather adorable at times, perhaps best shown by her love for fluffy animals and her attempts to relearn her smile.

Danganronpa 3: The End of Hope's Peak High School

The human Chiaki is a Gamer Chick who geeks out whenever someone recognizes the game she is playing but is no less adorable.
Mukuro Ikusaba gets easily embarrassed when asked to sing, blushes when talking to her sister and seem to sometimes not know what she should be doing.
Kazuichi is really proud of his work and likes to show it off to everyone. Just watch him rambling on about the giant TV monitor he builds in episode 2, even though it's obvious nobody is listening.
With her upbeat nature and quirky personality, Ibuki definitely qualifies in full contrast to her music and fashion sense.
Ryota really loves anime, and has piles of CDs of it in his room.
Seiko reacts with adorable glee when her drugs are effective, complete with Love Bubbles.

Danganronpa V3: Killing Harmony

Kaede has her moments. For example, during her Love Suite Event, she insisted that Shuichi should call her by her first name (in Japanese) or a pet name like "sweetheart" (in the English dub), but when he complies with her request, Kaede still gets embarrassed to hear him do it.
Shuichi's lack of social skills, innate kindness, and cute blushing sprite easily places him under this trope.
Himiko's laziness, outdated way of speaking and her other character quirks combined give her an unique cuteness when compared to the other characters.
Once you get past her aggressive, vulgar persona, Miu is a wacky science geek who doesn't know how to make friends.
Gonta is a young man who's been Raised by Wolves and learned to love insects, along with the desire to be a gentleman.
K1-B0 is a robot with No Social Skills, so it's natural he'd fall into this.