I would adjust beetles list to the following:
for resources the only ones with little to no opportunity cost when you settle on them is: copper/silver/gold/gems/iron hills and desert incense. Every other resources you settle there is an opportunity cost, some small others large.
Why are these basically no-brainers? Well for every tile you settle on you give up working it, so no matter what you don't want to settle on a resource unless it gives you an objective bonus (greater early yield). Then you want to make sure that bonus is greater then settling somewhere else and later working the tile. In the case of all the hills luxes as beetle says you give up 1 gold and 1 production from not being able to mine and work it. However, it is very unlikely you would have the spare food to work a no-food tile for a long time anyway. In the meantime you get the lux connected immediately without moving workers out there, get 2 gpt way earlier then you could have otherwise, and an extra +1 production to the base tile, along with extra city defense. I see iron/hill in the same category. For most of the game you only gave up 1 hammer from settling on it rather then working. You couldn't work it for a long time anyway since it has no food, and settling on it gives you 3 hammers, even better then a normal hill making your city produce stuff, much, much faster early. lastly, you can hardly ever work desert incense since it is a pure-gold tile. You can't afford to get only 3 gold for a citizen which hurts your food and production. But if you settle on it that tile suddenly becomes 2 food, 1 hammer, and 2 gold. You gave up 1 gold for 2 food and a hammer. This is a rare example of a net positive opportunity cost. Unfortunately unless the tile is coastal it's often in a bad spot to settle, but there have been a few times where it wasn't for me. Pretty much any tile with some base food is worth avoiding settling on as you get more yield by settling a worse tile and working it. An exception I might make would be if I was in plains and there were calendar resources about that would be hard to work due to their poor food. I might settle on one to get the early lux connection so I could put off researching calendar and get 2 gpt much earlier then usual. This does have an opportunity cost though of 1 gold but it gives you an extra 1 food in return. Even though this seems like a net win, it may not be enough to justify giving up the nice tile to work later. But given it's just gold and the city is food-poor it's not too bad of a trade. I may get a better city by settling the lux, giving up plantation, and farming the surrounding plains. It's basically trading gold for food which is a good deal. In the case of grass it gives you a trade of 1 gold for 1 hammer, but I find grass calendar resources workable much earlier then plains ones and these cities also aren't hurting for food so I am more reluctant to settle them. All this analysis excludes boosts to food/production that come in industrial as about 2/3 of the game is earlier then that.
Isn't settling on Deer make your city yield 3f 2h. Same as a Deer Camp? Again, depending on what that puts in your workable tile range, I think that's a good spot to settle.
Well usually it is a bad call in my opinion. I'll try to explain why: the way it works is the game clears all forest, jungle, marsh, etc, when you settle and looks at the base yield. If it is worse then 2f1h then it rounds it up to 2f1h. If you have more then 2f, more then 1h, or more then 0 gold, faith, culture, etc. it adds the extra amount to your base tile.
In the case of deer, deer add 1 food to the tile they are on and after the camp add 1 production to the tile. With a granary this becomes 3f 2h in forest or flat plains which is what you quote. However, if you clear and the underlying terrain was grassland it is 4f 1h.
Now, if you settle on it, the forest gets cleared and the base tile is 2f 1h on plains or 3f on grass, and 2f on tundra. You get no bonus whatsoever, therefore, for settling on a deer with underlying plains or tundra. You get a bonus of 1 food for settling on grass deer for a base tile of 3f 1h. Base tile deer are still buffed by granary but you always give up the yield from the camp so no matter what you'll never get 2 hammers out of the tile if you settle on it. You also won't get the extra +1 gold after economics. This is why it's a bad deal. At most you get 1 extra food from the base tile when you first settle on it, but you do lose hammers if it was a forest or plains deer. Camps come very early as well so you start operating on a loss if you settle on it very early. Also, since the food is always 2 or more the tile is better to work.
Even if it was break-even for the actual tile yield (like a flat tundra or grass deer) I wouldn't recommend it because you give up a nice tile to work so you end up losing. If you settle on the tundra deer in our example your base tile is 2f 1h (same as improving and working deer!) but your other tiles of tundra are worse. You would have been better off settling on and improving the tundra then working the deer so you have two 2f 1h tiles! Same goes for flat grassland deer. You could settle on the deer and get the same yield of 3f 1h as improving it with camp, however, if you settle somewhere else and work the tile, you end up getting an extra hammer out of the deal which in grassland is a better deal then just another flat farming site.
In general if you settle on something you want to think beyond the tile itself to the total effect on the city. Even if settling on it is the same as working it usually you are still losing something as resource tiles are nicer then normal tiles. You'd be better off settling and improving a bad tile or a hill if one is around for greater overall effect. If what you settled on would be hard to work anyway you give up almost nothing, and actually gain if the base yield is pretty good (some hill resources) reasoning cited above.
I omit sheep, stone, and marble from this category though. The reason being sheep tiles are very early workable at 2f 2h so better to not settle on it and work it. It is the earliest source of 2f 2h tile too so the net effect of leaving it and quickly improving/working it is better then any other. Someone cited an example of hills near water, but settling on the sheep is still worse in this situation because you don't get 2f 2h from the farmed hill till after civil service, which is way, way later then animal husbandry. You're giving up almost 80 turns of that extra 1 food doing it the other way around. Marble and stone I omit because even though they look like iron/hill they aren't Why? Because of stone-works. Stone works you can build super early and it buffs stone and marble by 1 and adds an extra happiness. But you only can do this if you have quarries and you can't build a quarry if you settle on them. So unlike iron settling on them you give up 2 hammer and 1 happiness if they were the only resources around. If there are 2 stone resources you still give up 2 early hammers instead of just 1 but it is an ok strategy if you don't have to give up stone works because there is another one nearby.
