beavers diverting rivers and such i can see, but creating sinkholes, overhangs, creating lightning rods to control and increase the likely hood of lightning strikes in sand, and a few others i don't see animals doing. and i am considering mega beasts as sentient for this purpose. in the past we have created anything from mountains to islands, diverted rivers, expanded and contracted deserts, forests, lakes, seas, oceans, etc.
it would be great to give the world a personality during worldgen, and possibly (later in the development cycle) while the player is playing. imagine a field of sinkholes left over from a war between dwarves and humans, and in checking the history logs you find that the dwarves, being outnumbered decided to create a 'minefield' between them and the nearest human settlement, so that most, if not all of their army would perish before it even reached their halls. or a small group of goblins on the run from some hunters, went into the desert at the beginning of summer, and created some overhangs so that they could survive in the deadly heat, so that when the hunters finally met up with them they were half dead already and the goblins easily won what should have been rather difficult battle. even non battle related stuff, like humans so in awe of finding a fulgerite where lightning had struck, that they began to place iron rods in the sand when ever a storm came in hopes of getting more, but these artificial fulgerites were shunned, so the humans that were trying to make a fortune off of the fulgerite sales, pulled their lightning rods leaving vast fields of fulgerites untouched. or a great dwarven caravan, laden with precious metals, gets washed away while trying to cross a river, and for decades afterward the settlement down river swells with people panning for these precious metals, all the while sending expedition after expedition into the barren mountain in hopes of finding imaginary deposits of gold and platinum.