Isekai has long since become one of the most popular anime tropes. Someone from our world is transported from our world to another, either real or virtual and gets stuck there. The problem with isekai, is that these anime have become so generic that that very few have any unique elements at all. Nowadays it's all Fenrirs, slimes, and life magic while searching for Japanese cuisine and building a harem.
These are 5 of the more unusual isekai anime.
Konosuba: God's Blessing on This Wonderful World!
Konosuba was the original anti-isekai, spoofing many of the common elements which make up the isekai genre. This was the original protagonist requests that the god come with him to the new world, only to find out she is useless. While watching it today it some elements may appear generic, that is because it came out early enough that everyone else is just copying it. Otherwise, the story is unique, with an unusual system of magic and gods and a rich history enriched by thousands of years of summoned heroes.
Re: Zero
Re:Zero is very unique. The protagonist gets a power over which he has no real control. When he dies he regresses to a point in the past with his memories intact. Nobody but him remembers what happened and the choices he makes affect the outcome for better or for worse. This is the somewhat similar in premise to The Vat of Acid episode from Rick and Morty, but this anime came out way earlier. What's interesting about Re:Zero is watching the protagonist in his attempts to move towards his goals and often failing. The storyline is surprisingly well fleshed out with many memorable characters.
So I'm a Spider, So What?
This is one of the more out there anime. A teenage girl is transported to another world where she is reborn as a giant spider monster in the middle of the most dangerous dungeon in the world. As she defeats and consumes enemies she continues to evolve and grow stronger while searching for her way to the surface. What's really great about So I'm a Spider, So What? is how it differs from the manga. The story is based off a light novel, so the anime and manga explore different areas, giving you a more comprehensive vision of the world.
Reborn as a Vending Machine, I Now Wander the Dungeon
This might just be the weirdest isekai on this list. While other anime usually feature human creatures, the protagonist of this one is literally turned into a vending machine in a dungeon. The world he is transported to is much less advanced too, so no one has any idea what a vending machine even is. As a vending machine, our protagonist levels up to include new food and drink items as well as potions and equipment. This is still somewhat of an action anime. A hot young woman picks him up and carries him around for buffs and supplies.
Saga of Tanya the Evil
The protagonist is the hatchet man for his company, an asshole that enjoys the power he feels from firing someone. After being pushed in front of a train by someone he just fired, the man meets god and proceeds to berate god proclaiming that there is no god. God enraged by this reincarnates the protagonist in a world at war as a little girl. One who will inevitably face divine wrath in a war on a highly religious version of the earth. Our protagonist then becomes the youngest child soldiers of the empire and tries to climb up the ranks to get a cushy job in the military, but is misunderstood as a battle crazed warmonger.
Uncle from Another World
This is an after the isekai anime. A young man's uncle wakes up after decades in a coma. Everyone else treats him like a crazy weirdo because the uncle keeps ranting about another world. We quickly learn that everything is true and that the uncle had one crazy adventure. The uncle can continue to use magic on Earth and projects scenes from his memories using magic. This isekai is unusual for several reasons. It is a post-isekai story, the protagonist isn't the person who was transferred to another world, and uncle was seen as ugly enough to be deemed a monster by virtually everyone there, including other monsters.
The Eminence in Shadow
A young man is reincarnated into a new world with one goal, to become the strongest and control the world from the shadows while pretending to be weak. As a child, the protagonist saves a young elf and convinces her that he is the leader of an organization formed to prevent the resurrection of a demon god. He is totally bullshiting, but as we find out all the things he is making up are actually happening. As the years progress the elf continues to save others and he does in fact become the leader of an organization. Everyone else takes it very seriously, but he thinks its all something he made up.