There is a way to spot fake gameboy cartridges.  I speak from experience for Gameboy Advance Games only.  Not Gameboy Color or DS cartridge games.  This guide is for only Gameboy Advance Cartridges only.  There is 2 things to look for.

First, there always is a number imprinted on the cartridge on the geniune ones.  Indented numbers.  You'd have to look at it at a certain angle or light to be able to see it.  Usually there are 2 numbers.  Such as "11" on the right side of the cartridge imprinted on the sticker part where it describes the name of the game.  If you do NOT see that, chances you have a fake one. 

Secondly, another way to be sure you have an authentic Nintendo cartridge is to look inside the cartridge.  If you look at the right angle again, you should be able to see "Nintendo" printed inside behind the ridges.  It's real hard to see but with a flashlight and a good angle, it's easy to spot.  If it's NOT there, it's fake!

These two are my basic ways of telling whether they are authentic.  Other ways may include the way the manual is printed or if the box comes in flat.  The fake ones usually tell you that the box will be flat to save on shipping. 

eBay has done alot in getting rid of the sellers who sell bootleg games.  There are less chances of getting a bootleg game now on eBay but before eBay booted these sellers, alot of people bought these games and those very people may be selling them back out when they're done playing with them or just for profit.  They may or may not know it's bootleg though. 

Update! 11/3/06 - I just found sellers from Thailand, China, Australia selling Gameboy Advance Games again! Beware! I'm almost pretty sure they are counterfeit.  There are clues there.  Some say, cartridge only, some are only a day auction.  (In the past, the counterfeit sellers only sold on 1 day auctions to lessen the chance of eBay pulling their auctions off)  You take a risk buying from them.  For some reason they are back on eBay.  I'm hoping eBay will get them soon.   

Buyer beware!!

Hope this helps!