The Ioun Stones comes from Jack Vance's Dying Earth series, which is where the "fire and forget" spell casting of D&D came from too, as well as some of the spells such as prismatic spray. The stones are harvested from the core of neutron stars that are being sliced away by the Nothing at the edge of the universe and are therefore rare and difficult to obtain. Their origin is dealt with in the Dying Earth collection Rhialto the Marvelous.
They were introduced in Issue #1 of Strategic Review (no author given, although there is a reference to Vance approving the design/inclusion and he and Gygax corresponded) and first made their way into the rulebooks with the original DMG.
These crystalline stones always float in the air and must be within 3 feet of their owner to be of any use. When a character first acquires a stone, she must hold it and then release it, whereupon it takes up a circling orbit 1d3 feet from her head. Thereafter, a stone must be grasped or netted to separate it from its owner. The owner may voluntarily seize and stow a stone (to keep it safe while she is sleeping, for example), but she loses the benefits of the stone during that time.
Ioun stones have 1 hit point, and an Armor of 5. The powers of each stone vary depending on its color and shape.
Example stones include:
Amber stone: adds 2 to armor class
Crimson spindle: grants user Infravision
Mirror pyramid: immune to petrification
Yellow sphere: sheds light (as per the rote)
Green star: immunity to poison
Green disc: you require no food, water or air
Red cube: immune to normal fire damage
Blue triangle: immune to charm and sleep spells
Dark blue rhomboid: you can never be surprised
Pale orange ellipsoid: feather fall (no damage from falling)