Crystal Balls are items that have been featured in many games throughout the Mario series. The first one was seen in Super Mario Bros. 2. Birdo spits it out after being defeated, and grabbing it opens the Hawkmouth to the next level. Years later, another one is seen in Paper Mario as the main magic tool for Merlon's family. There's also a red crystal ball, the Ultra Stone, for Ultra ranking Mario's partners. The Ultra Stone, as well as a standard Crystal Ball, is also seen with Merlon in Paper Mario: The Thousand-Year Door.
Madame Clairvoya used one to see the future and other things in Luigi's Mansion. Another was used in Mario Party 6, in the Seer Terror mini-game. Bowser used it to see a player's "future," which usually was something bad. Occasionally, however, the player received Coins or a Mushroom. All of this was just for fun, however, and had no effect on gameplay.
In Super Paper Mario, when Chapter 5 was complete, players could go see Merlee at Flopside. She claims that she wants her Crystal Ball back from Merluvlee, and wished the player to go get it for her. After doing the task, Merlee rewarded the player with a key that opened a storehouse containing Piccolo the Pixl.