From my childhood, two come to mind:

Carmen SanDiego games. I learned what spelunking was and some random facts about countries/states/history.

Amazon Trail. The player went on a research trip up the Amazon river. https://classicgames.gg/play/play-the-amazon-trail-online/

Slightly more recently: Typing of the Dead. This one probably leans much more towards a game with a gimmick, but touch typing was a good skill to have.

Math Blaster (1987 one)

Spent soo many hours getting good with the jetpack

They're not explicitly edutainment, but the Civilization games have a ton of historical tidbits that are just for general interest, rather than being part of the game.

I had a game growing up called The Way Things Work, which kept my attention for quite a while. Then I became an engineer, so maybe it's just me.

Where in Time is Carmen Sandiego…. At least nerdy kid me loved it. That may explain some things.

It wasn't advertised to me as an educational game, but "Dave the Diver" enriched my understanding and curiosity for various aquatic organisms! It was a fun adventure and I find myself recognizing things I learned about in the game elsewhere often, to my delight.

There is an old dos series called Gismos and Gadgets

Some of the 90s era educational games were pretty cool:

• The Dr. Brain series
• Logic Quest 3D - An edutainment FPS set in a medieval world with logic programming and voice acting. The controls were terrible.
• Stowawy! - Very minimal gameplay, but a great experience. I would kill for a 4K remaster.

Pharaoh/Cleopatra had lots of relatively in-depth explanatory text about life in ancient Egypt, but I don't know if it qualifies as an educational game.

When I started playing computer games, most of them were just text adventures and I had to read the text and understand it, and use context clues to solve puzzles.

Where in the World is Carmen San Diego was pretty big when I was a kid. It was pretty good at teaching you geography.

Number munchers.

Oregon Trail.

Where in Time is Carmen Sandiego?.

The incredible machine!

Yes, actually. The answer that comes to mind is Gilbert and the Chemystical Island - a game I spent a lot of hours with as a kid together with my parents. It's basically a Myst-like point-and-click adventure game with the usual trappings of "combine items and drag them onto problems on screen to solve", but where every problem has a solution rooted in science and chemistry intended to be a teaching aid.

I had a great time as a kid making batteries out of lemons and nails and learning about paper being made from trees and many more little discoveries.

When I was a kid, I used to play a lot of educational games. I had the various JumpStarts and was a big fan of Zoombinis. I learned a lot about ancient Rome from the Caesar series too.

As an adult, the Paradox 4X games (Crusader Kings, Victoria, Europa Universalis) can actually teach you a lot about history and geography. I mostly play the older ones because the newer ones have atrocious development cycles and DLC policies. Victoria 2 is my favorite!

As a kid I liked "Mario's Time Machine"

Oh yes. Colobot https://en.wikipedia.org/wiki/Colobot and Mind Rover https://en.wikipedia.org/wiki/MindRover were great fun.

The genetics in Niche are realistic enough the game could be used as a teaching tool for that, and as long as you're playing with a small tribe it can be rather fun. Just make sure you don't have a lot of nichelings, otherwise you'll hate yourself at the start of each turn (harvesting food is a chore).

Kerbal Space Program

As a kid Cluefinders was my jam. I spent so many hours on those and definitely improved in some topics thanks to them.

My childhood in the 90s/early 00s was chock full of them!

Reader Rabbit, Math Blaster, Carmen Sandiego, Dr. Brain, Sesame Street, Magic School Bus are some of the main ones that come to mind.

Freddy Fish and Putt-Putt feel like they may have had an educational component, the same studio had an edutainment game where you learn all about how airports work.

While not marketed as educational games, the impressions games (Caesar, Pharaoh, Zeus: Master of Olympus), Civilization, and Age of Empires/Mythology taught young me a lot about history.

The very first computer we got, an Acer Aspire running Windows 95, included a software bundle. One of those was Novell “Read with me 1&2” and “Memphis Math” The former was a series of mini/microgames to learn basic spelling and counting, the latter had 6 year old me struggling to grasp fractions (and eventually starting to figure it out before it was covered in school)

The Eyewitness encyclopedia / educational games were really cool too.

Mavis Beacon Teaches Typing had a bunch of minigames that got me the fast fingers I have today

The discovery tour of Assassin's Creed Origins.

The main game itself was boring and repetitive, but the discovery tour was fun and educational.

Chip Wits (for the Mac)

Dr. Brains Castle

The Incredible Machine

Orlando Poon's Toxic Ravine Cleanup and Rescue Service

One might argue that even DOS and Sierra Quest games were educational, in the sense that they certainly strengthened my English skills (who's not living in an English-speaking country).

Yes! Jumpstart 6th grade with Botley the robot was genuinely a fantastic educational game that I came back to play multiple times as a kid.

The Humongous Entertainment games (Spy Fox, Pajama Sam, Freddy Fish, Putt-putt) are also extremely polished educational point'n'click adventure games for young kids that I adored growing up.

Headline Harry and the Great Paper Chase

Not educational as such, but I played a lot of Star Wars: Epic Duels and Heroscape, and both of them rely on precise interpretation of the wording of powers. "May" vs. "Must", that sort of thing. It made me hyper vigilant of the exact wording of agreements, such that a contract lawyer once complimented my obsessive attention to detail in a contract. So I'd say that was pretty educational.