Mecha Bomber - Super Bomberman (SNES)
Black Bomberman gets abducted by Carat Diamond and Dr. Mook and his schematics are used to create an army of Mecha Bomber robots. They lack the more joyful look of regular Bomberman bots and have eye expressions that make them look downright evil. These fake Bombermen are also much more durable than the originals, able to sustain a heavy dose of damage before they can be eradicated. Just like the original Bombermen, these not-so-cheap knockoffs have an endless supply of bombs at their disposal. The Mecha Bombers are certainly some of the better bunch of clones in the gaming world. You may not remember Diamond and Mook, but you won't soon forget their sinister Mecha Bomber creations.
Les Enfants Terribles - Metal Gear Series (Various Platforms)
That's The Terrible Children for those of you that don't speak French. There is one highly convoluted back story behind the birth of these clones, so I'm gonna give you the abridged version. Big Boss was the world's best soldier but after being exposed to radiation for a second time, he was unable to produce offspring. Not wanting to let his legacy end with him and make sure the USA always had the best manpower, the government set out create clones of Big Boss with some heavy tampering involved. Three successful clones were made in total: Liquid Snake, Solidus Snake and Solid Snake. Liquid Snake believed he was given inferior genes and that Solid was given the superior genes, when in fact, the reverse was true. Liquid ended up resenting Solid because of this so he has issues. Serious issues. Solidus wound up becoming the figurehead of the world as the President of the United States and a terrible adoptive father to Raiden and Solid Snake, the most normal of the trio choose to fight for freedom, protecting the world time and time again. Each of the clones is highly intelligent and are experts at hand-to-hand combat, making them the best soldiers the world has ever known. Sounds like they got a good deal, right? Remember that tampering I mentioned earlier? Each clone was design with accelerated aging should they turn on their creators or fall into enemy hands. By the time Solid Snake is 42 years old, he looks like he's in his 80s and only has a year at best to live out his final days. Bummer.
SA-X - Metroid Fusion (GBA)
Tap, tap, tap, tap, tap. Do you know what that sound is? That's the sound of your doom slowly approaching. When returning from a mission, Samus is infected by the X Parasite, a creature that duplicates the host's physical appearance, memories and proceeds to terminate them after. The federation manages to save Samus' life with a vaccine the from Metroid hatchling from Super Metroid but the X Parasite's one weakness, the Metroids, have all been whipped out. To make matters even worse, when the X Parasite infected Samus, her power suit was at full power, meaning the SA-X has access to all of Samus abilities. When Samus is given her new mission, she's pretty much naked with a bare bones power suit. Oh dear. When I heard the background music dim and heard those footsteps, my heart was filled with dread. Playing Metroid Fusion and being confronted with the SA-X is one of the few times in gaming I've been legitimately frightened. Throughout most of the game, you are not match for the SA-X and you have to flee for your life until you're strong enough to take it out. And those eyes! Those horrible, soulless eyes! I Believe Question said it best in an episode of Justice League Unlimited. "Looking into those eyes was like looking into an empty pit."
Cosmic Clones - Super Mario Galaxy 2, Super Mario 3D Land (Wii, 3DS)
Nothing is more aggravating than trying to make your way through a level and having these little snots shadow you the whole way. They mimic your every move and have the most grating voice, very similar to Bowser Jr, a character I wholeheartedly despise. In Super Mario Galaxy 2, they come in groups and can make tricky galaxy stars all the more frustrating. In Super Mario 3D Land you only get pursued by a single Cosmic Clone but sometimes these things pull a "Magic wand, make my monster grow!" At least in 3D Land they can be killed with a Starman which is oh-so satisfying.
Dark Link - Legend of Zelda Series (Various Platforms)
You think you're hot stuff because you got a ton of achievements on (insert modern game here)? Just getting to the Great Palace in Zelda II: The Adventure of Link was bragging rights. It's like all those stories your grandpa told you about walking to school in 90 degree below blizzards, except they were all true. And when you reached the boss chamber, your own shadow jumps off of you and starts attacking. Wait, what? Yeah, it turns out Dark Link, your doppelganger is an even bigger threat than all the bosses you've faced thus far. Performing open heart surgery for the first time blindfolded is easier thank defeating Dark Link the fair way. The suicide rate probably skyrocketed when Zelda II was released. In 1998 players are struggling with the agony that is the Water Temple. "This dungeon can't possibly get any worse," you're thinking to yourself. And then the middle boss shows up. Guess who's back? I wonder, how many F bombs were shouted when gamers saw Dark Link again. As technology improved, Dark Link looked even creepier the more games he appeared in. It's becoming increasingly clear that as long as there are Zelda games, Dark Link will always be around to send shivers down our spines.
Sonic Robot Copies - Sonic Series (Various Platforms)
Dr. Robotnik (or Eggman if you must) has made some sinister creations, but by far, the doc's best work are the robot copies of the blue hedgehog he's tried so hard to kill over the last 21 years. First there was Silver Sonic (Sonic 2 on the Game Gear and Genesis) who looked intimidating at first but was quite easy to beat once you figured out his predictable pattern. Then there was Metal Sonic, the most well-known robot copy who kidnapped Amy Rose in his debut appearance in Sonic CD. Already I love this guy. Finally, there was Mecha Sonic, who was Knuckles final foe in Sonic 3 & Knuckles, and in a surprising turn of events could use the Master Emerald to transform into a super form like Sonic. Metal Sonic is my favorite of the lot, but I certainly wouldn't mind seeing Silver and Mecha Sonic make a much deserved comeback.
Gogo - Final Fantasy V-VI (SNES, PSX, GBA)
After the Apocalypse in Final Fantasy VI, a creature called Zone Eater can be found in the World of Ruin. Let Zone Eater inhale you and you'll see that it's quite spacey on the inside. A bit or roaming about and you'll find Gogo. Whether Gogo is a man, a woman, or human at all still remains a mystery to this day but what really matters is the skills that Gogo brings to the table. Gogo's specializes in mimicry. Gogo has the uncanny ability to copy whatever attack the previous party member used for the cost of nada. That's a pretty sweet but one could argue that it was done even better in Final Fantasy V. If you sought him out and defeated him, Gogo would award you with the Mime class, one of the best Jobs in the game. You could have one party member with the Gil Toss ability equipped and have three other party members use Gil Toss at the expense of just one dose of Gil. That's just a small example of how useful Gogo can be. Sure Gogo may not be as direct a clone as others mentioned here, but his Mime skill is the perfect embodiment of a clone.
Copy X - Mega Man Zero Series (GBA)
Neo Arcadia was the long awaited peace between humans and robots that Dr. Light dreamed of. It was ruled by his own creation, Mega Man X. But X sacrificed his own body to seal the Dark Elf. Not wanting Neo Arcadia to fall apart, Ceil built Copy X to rule in X's stead. While Ceil had good intentions, things did not go as planned and Copy X eventually became the new big bad to terrorize the land. In his own words, Copy X is a perfect copy of the original X. Except you know, Copy X is evil. He thinks he's never wrong and is very quick to act violently. Things got so bad that Zero was awoken from his long slumber to kill Copy X because the resistance couldn't handle him. X's ending to Mega Man X4 showed him worrying about the possibility of him going maverick and asking Zero to destroy him should that ever happened. The original X didn't go maverick but Copy X sure did so in a way, X's fears came true and like he asked, Zero took care of things for his old friend.
Omega - Mega Man Zero 3 (GBA)
Dr. Weil's finest creation, Omega starts out looking like a giant mech but once the armor comes off, he looks like a carbon copy of Zero (but with red eyes so we know he's evil). In actuality, Omega posses Zero's original body. So in other words, the Zero body that the player has been using is a facsimile. Long story short, sometime before the events of the first Mega Man Zero began, original Zero's soul was transferred into a duplicate body while Omega occupied Zero's original body. Weil drops this bombshell on Zero, much to the player's shock. Killing Omega, means destroying Zero's original body. X appears telling Zero what makes Zero who he is, his heart, his soul is what counts, so Zero goes ahead and kills Omega anyway.
Dark Pit - Kid Icarus Uprising (3DS)
You might think that with a name like Dark Pit that he'd be the big bad or at least the dragon, sent to wreak havoc and destruction. Yes, you fight him on more than one occasion and he has that classic bad boy air about him, but Dark Pit is actually an ally and a very well-rounded character. He has a strong sense of justice, doesn't believe in blind loyalty and isn't afraid to call the gods out on their actions. Born from the Mirror of Truth, Dark Pit may be a physical manifestation of Pit's inner feelings. Whatever the case, he's one of best "clones" in gaming as fan response to him as been overwhelmingly positive.