As of yet it has no use,but in 1.0.0 it will be used to make an eye of ender.
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To throw an Ender Pearl, simply put in on the bar on the bottom and, with it in your hand, right click. This will launch the pearl and teleport you where it lands. But be careful! you will take falling damage, depending on how far you throw the pearl. You cannot throw an ender pearl in creative mode.
With the ender pear you can teleport that costs you some hearts and you just need to right click, the eye of ender is used to track down the ender portal that leads to the ender dragon.
Simply right-click(or whatever the right click is configured to) in the direction you wish to toss the ender pearl to toss it. It does not work in Creative mode.
The ender pearl is used to locate fortresses that take you to the end an new world in 1.9.3 . You can get the pre releases on the internet.If you right click the ender pearl it will shoot of into the air you keep firing it until it drops down and does not move any more. Then you have to dig around until you find the portal that takes you to the end. BE WARNED there will be loads of strong mobs in the fortress so come prepared.\WARNING:The above answer is incorrect. It is only applicable for ender eyes. To teleport with an ender pearl, simply right click where you want to go. -2b3o4o
To make an ender chest, you'll need 8 obsidian and an eye of ender. It is very important that you make sure you have the eye of ender and not the ender pearl, don't be confused by the two! To make an eye of ender, you will need one blaze powder and the ender pearl. Blaze powder is made from one blaze rod (dropped from a blaze). Then, with the 8 obsidian, using the crafting table, you place obsidian in the same manner you would a chest, with all the boxes filled except the middle, the middle is filled with the eye of ender. I have provided the crafting recipe visual in the related links below!