Good point. I think the same folks made the Blupi (aka Eggbert, in the USA) games, Epsitec SA, which were legally made freeware a few years back. (or at least they initially developed Colobot but another team is handling it now I think)

http://blupi.org/

Not educatioanl specifically but they're very child-friendly platformers and puzzle games, and Speedy Blupi 1 and 2 have level editors which allow for creativity.

Buzzing Cars aka Wild Wheels is very fun too.

And now i have remember next games:
Bioscopia, Chemicus, Physicus and Geographicus. (1999-2004). I have never played these games but they are mostly well rated. Adventures where you solve puzzles in related categories.

E: I have found many more games of this kind:
Boscopia, Chemicus 1, 2, Geograficus, Physicus 1, 2, Mathica, Historion 1, 2, Informaticus, Technicus, Opera Fatal and probably many more. Look for Heureka-Klett / BrainGame Publishing GmbH publisher.
en.wikipedia.org/wiki/Heureka-Klett