Doppelgänger

"If you travel far enough you will eventually meet yourself."

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Doppelgänger was a word from the German language which meant an exact duplicate of a living person. The term doppelganger has been used throughout history, most often when someone met an identical copy of themselves who was not a biological twin. Currently, Miles O'Brien, Harry Kim, and Naomi Wildman are doppelgängers of their respective "originals". (DS9: "Visionary", VOY: "Deadlock")

Physical duplicates

James T. Kirk

In 2266, a transporter accident split James T. Kirk into separate "good" and "evil" personas. It was eventually discovered that the two could not live without each other, and they were reintegrated by the transporter. (TOS: "The Enemy Within")
Later in 2266, Kirk was again duplicated, this time in the form of an android, by Roger Korby and other androids on the planet Exo III. This duplicate was vaporized by Andrea, who mistook it for the real Kirk. (TOS: "What Are Little Girls Made Of?")

Spock

In 2269, a giant clone of Spock was created by Stavos Keniclius 5 and christened Spock 2. When the original Spock departed the planet Phylos, Spock 2 remained behind to work with Keniclius to work on a cure for a plague afflicting the Phylosians. (TAS: "The Infinite Vulcan")

Stavos Keniclius

Stavos Keniclius cloned himself several times in an attempt to find the perfect specimen to create a clone peace-keeping force. (TAS: "The Infinite Vulcan")

Jean-Luc Picard

In 2365, the USS Enterprise-D encountered a Jean-Luc Picard from six hours into the future. This Picard was killed by the current Picard, and then vanished. (TNG: "Time Squared")
In 2366, Picard was replaced by an alien copy; upon returning to the Enterprise-D, the real Picard commented that he "hoped his doppelganger hadn't caused too much trouble." (TNG: "Allegiance")
Sometime in the 2360s, the Romulans created a clone of Picard as part of a plot to replace him. This clone, using the name Shinzon, would eventually become the Praetor of the Romulan Star Empire before being killed by Data in 2379. (Star Trek Nemesis)

William T. Riker

In 2361, a transporter accident on Nervala IV duplicated William T. Riker, stranding one on the surface while the other left with the USS Potemkin. Eight years later in 2369, the Enterprise-D returned to Nervala IV and found/rescued "Thomas Riker". (TNG: "Second Chances")

Because the split between signals resulted in an equal distribution of Riker's transporter pattern, both of them had an equally legitimate claim to being the "real" William T. Riker, however it can be argued that "Thomas" is the real Riker as the transporter chief aboard the Potemkin used a second beam signal to retrieve the current person known as William T. Riker while the original beam signal rematerialized on the planet surface.

In 2365, the Mariposans stole Riker's DNA and created a clone from it. This clone was killed by the original Riker. (TNG: "Up The Long Ladder")

Katherine Pulaski

In 2365, the Mariposans stole Dr. Pulaski's DNA and created a clone from it. This clone was killed by the original Pulaski. (TNG: "Up The Long Ladder")

Miles O'Brien

Miles O'Brien was killed in 2371, after becoming infected with delta-series radioisotopes following an accident aboard Deep Space 9. He was replaced by his future self from a few hours later, making the current O'Brien a doppelgänger of the "original." (DS9: "Visionary")
A replicant of O'Brien was created by the Parada government, possibly to assassinate someone at the upcoming peace talks on the station between the government and rebel forces. This O'Brien died never knowing he wasn't the "real" one. (DS9: "Whispers")

B'Elanna Torres

In 2371, the Vidiian Sulan used a genotron to extract B'Elanna Torres Klingon DNA, leaving her fully Human, and then reconstitute a fully Klingon version of her. The Doctor was able to reintegrate B'Elanna's Klingon DNA into her Human self after her Klingon half was killed escaping the Vidiians. (VOY: "Faces")

USS Voyager

File:Voyager divergence field.jpg

Graphic of Voyager being duplicated by a subspace divergence field.

The entire crew of USS Voyager was duplicated by a spatial scission in 2372. The "second" Voyager self-destructed to destroy a Vidiian starship attacking them. (VOY: "Deadlock")

Harry Kim

The "real" Harry Kim was killed on Voyager when he was pulled through a hull breach on deck 15. He was replaced by the other Harry Kim from the "second" Voyager, making the current Harry a doppelgänger of the "first." (VOY: "Deadlock")

Naomi Wildman

The "real" Naomi Wildman died of complications due to hemocythemia. She was replaced by the "second" Naomi Wildman for the other Voyager, making the current Naomi a doppelgänger of the "first." (VOY: "Deadlock")

Iliana Ghemor

(DS9: "Second Skin")

Shapeshifters

Chameloids

A chameloid impersonated captain James T. Kirk during his imprisonment on Rura Penthe. (Star Trek VI: The Undiscovered Country)

Coalescent organism

A coalescent organism was responsible for the duplications and deaths of at least one Starfleet officer and a pet dog. (TNG: "Aquiel")

Changelings

Changelings replaced, or impersonated, a number of individuals in the years leading up to, and during, the Dominion War. (Star Trek: Deep Space Nine)

The Silver Blood

The biomimetic lifeform known as the Silver Blood duplicated the entire USS Voyager crew, and eventually the ship itself. (VOY: "Demon", "Course: Oblivion")

Illusionary

Leonard McCoy

Leonard McCoy M-113 creature (TOS: "The Man Trap")

Nancy Crater

Nancy Crater M-113 creature (TOS: "The Man Trap")

Deanna Troi

Nagilum (TNG: "Where Silence Has Lease")

Data