In total there are 102 Gems and 16 Boos that you need to find.
When you have all of them, you will be awarded with two special items: A new light for Luigi's Flashlight, and a crystal attachment for the plunger weapon. The special light shows an image of a Boo in the middle of your light. The crystal attachment is just a skin for the plunger.
Both items are purely cosmetic, but they do really look cool. Unfortunately there are no secret areas, cutscenes or anything like that tied to them.
You can get the new light for Luigi's Flashlight when you have captured all 16 Boos.
You can get the crystal attachment for the plunger when you have found all 102 Gems.
The bad part about this is that you are essentially finished with the game when you have all 16 Boos and the 102 Gems, so you likely won't have anything at all to do with your new cosmetic items.