Apart from the land before time I really like the animals of farthing wood, talespin, and a couple of other series of which I don't know how well known they are in the English speaking world.
Does anyone know Alfred J. Kwak? Though it is "childfriendly" it is quite educational with many parallels to our world dealing with problems such as polution of the environment, the danger of dictatorships etc.
There was also a whole series of cartoons which were like documentaries for kids (so the knowledge was wrapped up in stories), for example: "Es war einmal der Mensch" (the title is difficult to tranlsate as "es war einmal" is the traditional beginning of a fairy tale in German similar perhaps to your "once upon a time", so it might be translated as "Once there was the human" but in this case the past tense might sound a bit eerie in English implying there is no human anymore, an effect that would not occur in German) which is about human history, "Es war einmal das Leben" (Once there was life) about the human body, and "Es war einmal Amerika" (Once there was America) about American history. Those cartoon series were really cool, but I don't know if they were ever translated at all.