Hello, I'm in the very same situation, I'm missing just 1 gem and after 3-4 hours looking for it I finally came here for help.
Right now I beat the casino and have its gem (which should be the #200). I'm pretty sure the gem I'm missing isn't in the overworld, so it must be inside a cave/house/dungeon, but:
I've checked all the dungeons (more than once)
I've got the two from ganon's castle second floor.
I've entered all houses in the 3 towns in the 3 time periods and the gem detector is green.
Also checked tingl'es house, blacksmith house, boat man house, bridge man house.
Lost woods: I have the overworld ones for the 3 periods, two from the cave at the beginning (grappling hook, past and present), and the one from the sword cave (past).
The mine is green.
The graveyad one in the present (the one you have to use the bomb).
The passage to the pyramid (present) is green.
The southeastern cave in the desert is green (both past and present).
Witch house (blue potion) is green
I can't think of more places right now, but I'm becoming crazy looking for that gem!
EDIT: Here's my savegame if anyone is interested:
https://www.dropbox.com/s/2zv8n10ngkabq ... T_SAVE.rar