3) Dark Samus
Featured In: Metroid Prime 2: Echoes (2004)
So yes, we've already gotten a Samus doppelganger in the form of the SA-X, but the way Dark Samus is presented gives the character a sense of originality anyway. And while Dark Samus is present in Prime 3 as well, I'm focusing specifically on (her?) appearance in Prime 2.
The Space Pirate logs suggest that they were perplexed (and somewhat horrified) about the idea of there being two "Hunters", and any that attempted to stop her from stealing their Phazon were dealt with swiftly. After witnessing the first battle between Samus and her evil copycat, the Pirates considered trying to form an alliance with Dark Samus but this never panned out.
Over the course of Prime 2 you fight Dark Samus a total of three times, with each duel getting progressively more intense as she utilizes dark versions of many of your techniques (plus many Phazon based ones). The first fight takes place in the Space Pirate base, while the second takes place on a giant elevator in the Sanctuary Fortress.
Once the Emperor Ing has been slain and the final Light of Aether recovered, Dark Aether begins to destabilize and implode on itself. Just when you've reached the exit, who should appear but Dark Samus to stop you? This last fight is one of my absolute favorites due to its intense nature, coupled with the fact that the countdown timer to Dark Aether's destruction doesn't stop.
Once you've defeated your dark counterpart a final time, you manage to escape Dark Aether just as it is destroyed. After bidding farewell to the grateful Luminoth, Samus departs in her ship for her next mission. However, Phazon particles begin to form a familiar shape just outside of Aether's atmosphere...
3) Nightmare X (Metroid Fusion)
The Nightmare X is such a fun, and hard boss fight. Keyword being hard. I can't tell you how many times I died the first time I played this game. Despite being frustrating, this fight is great. Not only is the fight fun and hard, but the nightmare X looks really creepy. His face is scary looking, which is probably what you would expect from someone named nightmare. This fight is great and one worth experiencing. That's why it's number 3.