The cartridges fail to fit smoothly in the slot.
You are getting a non-official box.
The manual is usually home-printed (as well as the sticker on the cartridge).
They sometimes fail to work on new versions of the console (DSi).
(I used to buy a lot on second hand, and unfortunately I got 2-3 fake games like that)
gaming.stackexchange.com/users/69/Gnoupi
More than one game in a cartridge is a dead give away.
Some games have identifying features.
E.g. Pokemon games for GBA are transparent and coloured, while the DS games HeartGold/SoulSilver are black instead of grey, to allow for the Pokewalker's IR receiver.
gaming.stackexchange.com/users/109/Macha
Ways are: There are far more games contained in that cartridge.
(1 game vs. 25-in-one cartridge)
The cartridge back-side screw is not the same as the original screw
There is another splash screen that loads prior to the official Nintendo screen.
There is no official box, or the box received is different than the official box.
The cartridge is bigger than normal, or odd-sized, or is different grey colour than normal cartridges.
The seal 'Nintendo seal of quality' is faded or not present.
The game responds more sluggish than normal.
Cartridge Examples are: You buy a 2nd hand game, the cartridge received looks bigger or different shade of grey than the normal grey colour.
Gameplay Examples are: The gameplay responds much slower than a normal game would.
Playing Super Mario Boss GB, you keep falling down instead of jumping.
The game keeps saying 'Battery or CMOS corrupt'.
Your Zelda save-game keeps getting reset, or corrupted.
There is a loader (e.g., Hacked by XXXX team) that occurs before the official Nintendo screen.
If you are buying used GBA or DS cartridges, safe and advisable way is to: 1) Ask the person to take a high-resolution screenshot of the cartridge against a background you specify, example, 'YourName', 'YourAddress', so that you know what you are buying is what you are getting.
2) You might want to ask him to take a video of: putting the game in and out of the box
take a 360 degrees pan and zoom on the box, take a pan and zoom the cartridge, take a pan and zoom near the screws, move the camera around the seal of quality, take the into his/her GameBoy and the first 30 seconds of himself playing the game.
Pay careful attention to the box, the cartridge size, the unique background you have pre-agreed to and action putting in and out of the GB device.
gaming.stackexchange.com/users/72274/buttercup
On the Nintendo DS carts, I believe there's a series of numbers and letters printed on the green part of the contacts.
Also, the Nintendo logo is on the back (you can only view it at certain angles), and something like a serial number is stamped on the back.
For official GBA carts, the Game Boy Advance logo is faintly visible above the sticker, and the Nintendo logo and model number are on the back.
I can't confirm that pirated games won't have these features, but I'm pretty sure they wouldn't.
gaming.stackexchange.com/users/18/Kevin Yap
Another way to tell is that they do not in fact contain the full game.
gaming.stackexchange.com/users/320/Ritwik Bose
How can I tell if used GBA/DS games are pirated?
How can I determine if a used game is pirated?
gaming.stackexchange.com
<nintendo-ds><game-boy-advance>
gaming.stackexchange.com/questions/1355
gaming.stackexchange.com/users/299/averyzoe
The cartridges don't fit smoothly into the slot and the box is not official. They also might not work on newer versions of the console. The cartridge could also be bigger or a different shade of grey. They sometimes fail to work on new versions of the console, fail to fit smoothly in the slot, come with a non-official box, home printed manual and cartridge sticker. The cartridge may be a slightly different size or colour. More than one game in a cartridge is a dead give away and often it is not the full game. Some games have identifying features. On the Nintendo DS carts, there are a series of numbers and letters printed on the green part of the contacts. Also, the Nintendo logo is on the back and something like a serial number is stamped on the back.  For official GBA carts, the Game Boy Advance logo is faintly visible above the sticker, and the Nintendo logo and model number are on the back.  
They sometimes fail to work on new versions of the console, fail to fit smoothly in the slot, come with a non-official box, home printed manual and cartridge sticker. The cartridge may be a slightly different size or colour. More than one game in a cartridge is a dead give away.    Some games have identifying features. On the Nintendo DS carts, there are a series of numbers and letters printed on the green part of the contacts. Also, the Nintendo logo is on the back and something like a serial number is stamped on the back.  For official GBA carts, the Game Boy Advance logo is faintly visible above the sticker, and the Nintendo logo and model number are on the back.   Another way to tell is that they do not in fact contain the full game.