Manga

Zombiepowder by Kubo. It was cancelled but I wholeheartedly believe it deserves not only to be resurrected, but animated as well.

Top 3 entries from some of my MangaDex 10 / 10 lists (based on difference between my rating of 10 and the actual rating), with shitty descriptions:

Completed

A Complicated Sibling Relationship 4-Koma

• rating: 7.79 (difference: 2.21)
• greatest trainwreck I have read

I Guess I Became the Mother of the Great Demon King's 10 Children in Another World

• rating: 8.16 (difference: 1.84)
• MC pops babies out like nobody's business to save the world; the kids are cute though

I Decided to Fake a Marriage with My Junior to Shut My Parents Up

• rating: 8.20 (difference: 1.80)
• MC turn lesbian to stay with her roommate

Ongoing

Crossdressing Quest

• rating: 8.12 (difference: 1.88)
• MC awakens to something on his way to save the world

The Magical Girl ♡ In Her 30s

• rating: 8.37 (difference: 1.63)
• title describes itself

The Gals Who Always Say Insane Things: My Daily Life at a Private Paranormal High School

• rating: 8.44 (difference: 1.56)
• gals use superpowers for random BS

Kinda NSFW

Don't Call Me a Naked Hero in Another World

• rating: 7.09 (difference: 2.91)
• MC gets isekai-ed with only her bath towel

Rosen Garten Saga

• rating: 8.84 (difference: 1.28)
• most sexually deviant manga I've read

no third entry due to a lack of 10s

Here's a list of the stuff I tend to link from time to time. They're not perfect and vary on how underrated they are but all of them managed to stay with me in one way or another so that's something.

• Sui and Neri of the Twilight Planet - a cute (and short) slice of life series about a girl and a talking sloth running an inn on a dying Earth. Art reminds me of Girls' Last Tour (also read that if haven't and want some post-post-post apocalyptic adventures).
• Satellite Coin Laundry - sci-fi comedy about a space laundromat. It has some great panels as well as interesting aliens and ideas. Translation doesn't update particularly often unfortunately.
• Traveling Gyaru - fun travel story about a gyaru who decided to bike through a good chunk of Japan for her friend's wedding while knowing nothing about traveling on a bike. Nice art, interesting trivia about traveling and locations but not fully translated (last mangadex updated was over 2 years ago).
• I also like your flaws - an awkward boy and an amputee girl meet during their first day at school, start hanging out. It's a oneshot and could use a serialization to expand on the characters but it's a neat read.
• Pen Pal at the End of the World - another oneshot, this time about a young girl and a former artist exchanging letters in a post-apocalyptic setting.
• The Boy Who Collects The Stars - a short, magical story about a search for a mythical six-legged deer.
• The Unwomanly Face of War - World War II stories from a perspective of women who served in the soviet army. A unique look at a "overplayed" topic. Based on a book with the same title.
• Kowloon Generic Romance - romance, drama, sci-fi? It's a slow burn series about life in modern day Kowloon. It has both goofy and striking panels, some a bit more risque but don't expect a lot of fan service. It also has an official English release.

Finally, read Girls' Last Tour everyone. It's good. Read it.

The Voynich Hotel is a wonderful manga that i never see talked about. An ex-yakuza goes to a small island to escape his past and stays in the titular hotel. It's a slice of life manga in a world that is very weird.

@Weebdeluxe

I'll take this to mean both underrated (I gave it a rating decently higher than mean/median) and also ones that are not popular.

- Champagne If you've ever thought of reading Bartender but want to try something shorter, this is a good introduction. The ending, while a reasonably common trope, still kind of surprised me.
- Kako and the False Detective Another short read that sticks the landing. I don't know much about mystery/supernatural manga, even including body horror, which this isn't, but it was enjoyable. I liked Kako's character and design, and the plot is good.
- Sleepy Barmaid (ongoing) One of my true favorites. MC lives to the beat of her own drum.

Mieruko-Chan, or Girl who can see it

It's a comedy/slice of life (imo) with horror aspects. A girl is suddenly able to see spirits/ghosts one day, and tries her best to pretend she doesn't see them. I love it because each arc and Mieruko's intentions are so wholesome & end in building way more on spirits' rules and lore. The first few chapters do play on echi themes, but the author finds his footing for a plot once the first antagonist appears. Antagonist is not the right word, but I don't want to spoil character development details much. :x

I always dig Franken Fran. It's dark and edgy and seems to have been cut off before it's proper conclusion.