Normally when you try to collect more than 999 gems, the game will stop you from collecting more. However, if you play certain minigames (such as the race against Rottytops once you've gotten the Simmer Stone,) and earn past that limit, the counter will begin to display odd characters instead. Using this method it's possible to collect over 999 gems, and the game will keep track of the number. To get the counter to return to normal, simply spend gems until you have 999 or less gems left available.