The Gem Mines located north-east of Ponydale are filled with tunnels and glowing crystals. The entirety of the Gem Mines is roofed over, limiting the height a Pegasus can fly. There are only a few areas where the ceiling is high enough to hover well above the ground to evade ground mobs.
Rubies that can be picked up spawn occasionally in specific caverns. More precisely, the Northern Chamber when you first encounter Lantern Monsters, just after the chamber with Manticores and Husky Diamond Dogs. They will be collectibles on the ground, however, despite rubies being red, they currently hold no specific color and can be blue, yellow, green, etc.