Fountain of Youth, Uluru, Sri Pada, and Mt Kilamanjaro are my favorites. Great Barrier Reef is about is good too seeing as how you get 2 of them every time you find it, so it's essentially double what is listed. FoY is like getting a free +10 happiness, don't even need to work it. Also your troops double-heal all game. LIke WHAT? It is game-breaking. Uluru and Sri Pada cover themselves on food and give an essentially free religion. Sri Pada is a little less faith but the instant +2 happiness probably makes it even better. Mt. Kilamanjaro is less in yield but it covers itself with +2 food and a tidy early +3 culture which is nothing to laugh at. However, like FoY it gives an insanely powerful upgrade to all your units that get near it, making sieges on cities surrounding hills cake. really changes the game.
Barringer Crater, Grand Mesa, Old Faithful are pretty awful. It's nice to have old faithful in your territory for the instant +3 happiness, but working it? Who wants a tile with only a flat 2 science and nothing else? That's awful. Your city will never grow and a science specialist is more than twice as useful seeing as how you get more science points and an additional +3 GS points. Just a wasted spot in your ring. Barringer crater is +2 gold +3 science. It is decent as a tile, but I always seem to nerf my city more than it is worth working it. It needs a little food on it to be useful. Grand Mesa: same. No science but +2 production and +3 gold. It's kinda like a fancy hill so I don't mind it as much, but it also nerfs your early growth. Both of these are only worth it if I can get a food ship to cover their growth opportunity cost.
The only game old faithful was remotely useful to me was a game where it was in the 4th ring of a city way out in the ice. My city beelined it in natural expansion for +3 happiness, but it was too far out to even consider working and didn't waste a spot in my ring. It really needs a buff of +2 food or something. And I think to balance NW, that you should be denied the happiness unless you are working these tiles. You can't really compare apples to apples when some NW's give you effects immediately just for being in-borders and others don't. I also think NW's should get some tourism on the tile later in the game--maybe around the time of airports. It would make them more useful to work.