World War 2
Message To Adolf
Adolf Kaufmann is a reluctant member of the Hitlerjugend while Adolf Kamil, his best friend, is a Jewish refugee. As the fires of World War 2 rage on, destiny pulls these boys into their respective directions; threatening to destroy their friendship.
Osamu Tezuka’s Message To Adolf is a gripping story filled with conspiracies and intense drama. A story which is especially notable for its harsh critiques of fascism and the policies of Imperial Japan.

Grave of the Fireflies / Barefoot Gen
I group these two together, as they represent very similar themes. Ghibli’s Grave of the Fireflies and Keiji Nakazawa’s Barefoot Gen both tell emotional stories of children whose lives are shaped by the allied bombings of Japan. The former telling a story of siblings who are displaced by the fire bombing of Kobe, while Barefoot Gen chronicles the impact of the nuclear bomb on Hiroshima. Both movies are heralded for their historical authenticity and tragic storylines. I can attest to that, as both films left me a depressed husk for days after watching them.

Zenon
In a similar vein, 1999’s Zenon: Kagiri Naki Ai ni tells the story of Zenon Zebrowski; a Polish missionary who was in Japan in the aftermath of the nuclear bombs. Zenon Zebrowski was a real person, with this movie acting as a slightly-dramatized retelling of his charity work. Mainly focusing on his efforts to ease the suffering of the orphans left behind by the war.
This becomes a touching story of a man’s undying resolve to help others, no matter the setbacks faced along the way. A truly inspiring tale of a real Christian hero.

The Diary of Anne Frank
The Diary of Anne Frank is a movie about the life of Anne Frank, a Jewish refugee living in Amsterdam. As The Netherlands falls under Nazi occupation, the Franks go into hiding alongside other Jewish families.
These events are all based on the descriptions by Anne as collected in her now world-famous diary. As such the story isn’t exactly intense, but does feel very personal. It gives a unique perspective into the anxiety felt by everyday people as they are forced into inhumane circumstances. For reasons that are entirely beyond their control and entirely senseless. It is very powerful.
Japanese History
Data Masamune / Takeda Shingen
Written by the late Mitsuteru Yokoyama, Date Masamune and Takeda Shingen are biographical manga about these titular, historical figures. They cover everything from their childhood all the way until death, as events of great historical significance unfold around them. These manga are exceptionally detailed accounts while also being entertaining to read.

Hyouge Mono
Furuta Sasuke was a real-world statemen during the Sengoku era, who is most renowned for his contributions to tea ceremony. Though including a lot of fictional influences, Hyouge Mono broadly covers his rise to prominence and efforts to leave his artistic marks on Japan’s culture. Though not an action anime per say, these efforts are cast against the backdrop of the wider conflict raging across Japan at the time. This provides an interesting perspective about a lord who values culture and intellectual pursuits, but is nevertheless expected to partake in military conflicts.

Taisho Baseball Girls
Not capturing the story of any person or event in particular, Taisho Baseball Girls is instead a delightful sports anime set in an interesting period. The Taisho era of Japan is one renowned for its major cultural developments. It was a time of rapid modernization, as well as a broadening of Western influences in the historically-isolated nation.
Taisho Baseball Girls explores this setting through the lens of women’s sports. As a ragtag band of girls put together a baseball team, hoping to prove their skill against male peers. While doing so, the story constantly touches on the shifting of societal norms of the time. It’s A League of Their Own but with kimonos.

Diverse
Josephine the French Rose
In a rare shoujo example, Josephine the French Rose is a romance manga starring Joséphine de Beauharnais. A woman who would become the first wife of Emperor Napoleon and survivor of the Reign of Terror. Her story is a thrilling one filled with near-death experiences, heartbreak, and political turmoil. At the same time, this manga touches on the military exploits of Napoleon and the efforts of political figures like Robespierre.

Genghis Khan
Once again coming to us from the mind of Mitsuteru Yokoyama, Genghis Khan takes his biographical style of manga and applies it to a non-Japanese figure. It instead tells us about the legendary life and battles of Temüjin. The infamous warlord that we know today as Genghis Khan. Like his other work, Genghis Khan does a phenomenal job of humanizing historical figures. It takes a larger-than-life conqueror and tells his story in such a way that you end up with new, more sympathetic perspectives on the guy.

Hetalia
Finally, there is Hetalia. A series where every country in the world is personified as goofy anime characters, with world history playing out as increasingly-absurd feuds between them. The series covers a wide spectrum of historical events. From familiar topics like the world wars and American revolution, to now-ancient diplomatic rows over trade disputes.
Despite its silly exterior, Hetalia makes it easy to get a surface-level understanding of a broad spectrum of world history.

That’s a good list. I do want to make one correction that Grace of the Fireflies involved the firebombing of Kobe and not Tokyo for that specific story. Some other interesting historical anime/manga I can think of would be Yugo the Negotiator, Princess Kaguya, and Town of Evening Calm to name a few.
Thanks for the correction. Not sure how I mixed that up, but edited the error now. I’ll also take a look at your suggestions!
No problem. I’m glad I can help. Those were a few that came to mind. Town of Evening Calm is from the creator of In This Corner of the World which is another manga/anime that dealt with Hiroshima.