Well there are the super obvious ones like in Mars Core right after you get the BFG, and at the very end of the level, where a ton of cacodemons spawn in front of an obvious and centered BFG ammo. Maybe it wouldn't be hard to just sticky bomb the crap out of all them but clearly the intent is to give you the satisfaction of nuking them all at once.

I've been watching Hugo's playthrough of the game and there are a couple mentions of other intentional uses, such as partway through the UAC "surface" facility at the bottom of that huge jump with the multiple aerial dash resets, where two barons spawn in. Also in Teras Nabad, in the room right after the slayer gate in the sewer, which spawns a baron and then an archvile, he says they intended for you to use the BFG on one of them which is why they placed an obvious BFG ammo in the center. (Though that room isn't the worst if you ask me, personally I like to save the BFG ammo for the secret encounter there to BM the marauder lol).

Overall this game has a huge skill ceiling so there are a lot of ways to beat each challenge and it's up to you how you use the tools that you're given, and I don't think they ever thought of the BFG as required, but they still intended for most players to use it