List of rewards available by re-playing episodes at level 50.  All items are Mk XI rare (blue) unless otherwise stated.  Anything below Mk XI and below rare are ignored, as you can just get gear as good as or better than Mk XI green off the exchange for cheap.

For most of these episodes, you can only choose one of the listed rewards per playthrough; you need to re-play the mission multiple times in order to get multiple rewards.  For example, if you wanted eight of the Retrofit Phaser Banks, you would need to re-play "Everything Old Is New" eight times.

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Federation episodes:

The Doomsday Device
Hargh'peng Torpedo Launcher Mk XI (purple)

Past Imperfect
Efficient Impulse Engines Mk XI
Paratrinic Shield Arra Mk XI
Plasma-Disruptor Hybrid Beam Array Mk XI
Plasma-Disruptor Dual Cannons Mk XI

Project Nightingale
Plasma Beam Array Mk XI [Acc]x2
Dual Plasma Beam Bank Mk XI [Acc]x2
Plasma Dual Heavy Cannons Mk XI [Acc]x2
Plasma Torpedo Launcher Mk XI [Acc]x2

By Any Means
Regenerative Shield Array Mk XI [Reg]x2
Resilient Shield Array Mk XI [Cap][Reg]
Shield Array Mk XI [Cap][Reg]
Covariant Shield Array Mk XI [Cap]x2

Ghost Ship
Chroniton Torpedo Launcher Mk XI [CrtD]x2
Chroniton Torpedo Launcher Mk XI [CrtH]x2
Chroniton Mine Launcher Mk XI [Dmg]x2
Chroniton Min Launcher Mk XI [CrtD]x2

S'harien's Swords
Numiri Regenerative Shield Array Mk XI
Combat Hyper-Impulse Engines Mk XI
Prototype Gravitic Modulation Impulse Engines Mk XI (purple)

Shutdown
Resilient Shield Array Mk XI [Cap][Reg]
Covariant Shield Array Mk XI [Cap][Reg]
Shield Array Mk XI [Cap][Reg]
Regenerative Shield Array Mk XI [Cap][Reg]

Tear of the Prophets
Console - Tactical - Warhead Yield Chamber Mk XI
Console - Science - Stealth Module Mk XI
Console - Engineering - Monotanium Alloy Mk XI
Console - Science - Shield Emitter Amplifier Mk XI

The Other Side
Resilient Shield Array Mk XI [Ap][Cap]
Covariant Shield Array Mk XI [Cap]x2
Shield Array Mk XI [Ap][Reg]
Regenerative Shield Array Mk XI [Reg]x2

Cage of Fire
Chroniton Mine Launcher Mk XI [CrtD][CrtH]
Chroniton Torpedo Launcher Mk XI [CrtD][CrtH]
Chroniton Mine Launcher Mk XI [Dmg]x2
Chroniton Torpedo Launcher Mk XI [Dmg]x2

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Klingon episodes:

Second Star to the Right, Straight on 'til Morning
Efficient Impulse Engines Mk XI
Plasma-Disruptor Hybrid Beam Array Mk XI
Plasma-Disruptor Hybrid Dual Heavy Cannons Mk XI

Blood of the Empire
Console - Engineering - RCS Accelerator Mk XI

Destiny
Numiri Regenerative Shield Array Mk XI

A House Pursued
Hargh'peng Torpedo Launcher Mk XI (purple)

House On Fire
Disruptor Turret Mk XI [Acc][Dmg]

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Romulan episodes:

Smash And Grab
Efficient Impulse Engines Mk XI
Plasma-Disruptor Hybrid Beam Array Mk XI
Plasma-Disruptor Hybrid Dual Heavy Cannons Mk XI

Tradecraft
Paratrinic Shield Array Mk XI
Hargh'peng Torpedo Launcher Mk XI (purple)

Enemy Action
Tal Shiar Tachyon Deflector Array Mk XI

Revelation
Dynamic Reroute Impulse Engines Mk XI

Mind Game
Disrupting Photon Torpedo Launcher Mk XI

Last Stand
Caustic Plasma Beam Array Mk XI [Acc]x2
Caustic Dual Plasma Beam Bank Mk XI [Acc]x2
Caustic Plasma Dual Heavy Cannons Mk XI [Acc]x2
Caustic Plasma Turret Mk XI [Acc]x2

The Best Defense
Console - Engineering - SIF Generator Mk XI
Console - Science - Particle Generator Mk XI
Console - Tactical - Directed Energy Distribution Manifold Mk XI

Devil's Choice
Dual Injection Singularity Core Mk XI [SingA][SingC][SST]
Shield Array Mk XI [Cap][Reg]
Shield Array Mk XI [Cap][Pla]

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Episodes available to all three factions:

Installation 18
Piercing Tetryon Turret Mk XI
Piercing Tetryon Dual Cannons Mk XI
Piercing Dual Tetryon Beam Bank Mk XI

Coliseum
Reman Prototype Covariant Shield Array Mk XI
Resilient Shield Array Mk XI [Pla][Tet]
Combat Impulse Engines Mk XI [Full][Turn]

Cutting the Cord
Tractor Beam Mine Launcher
Plasma Torpedo Launcher Mk XI [CrtD][CrtH]

Skirmish
Covariant Shield Array Mk XI [Cap]x2
Regenerative Shield Array Mk XI [Reg]x2

Everything Old Is New
Retrofit Forward Phaser Bank XI [CrtH][Dmg]
Retrofit Aft Phaser Bank XI [CrtH][Dmg]
Phaser Beam Array Mk XI [Dmg]x2
Phaser Beam Array Mk XI [CrtD]x2

The New Link
Polarized Dual Tetryon Beam Bank Mk XI
Polarized Tetryon Beam Array Mk XI
Chroniton Flux Torpedo Launcher Mk XI

Operation Gamma
Jem'Hadar Combat Impulse Engines Mk XI (purple, Jem'Hadar set)
Jem'Hadar Deflector Dish Mk XI (purple, Jem'Hadar set)

Boldly They Rode
Jem'Hadar Resilient Shields Mk XI (purple, Jem'Hadar set)
Dominion Polaron Beam Array Mk XI
Dominion Polaron Dual Cannon Mk XI

Where Angels Fear To Tread
Shield Array Mk XI [Ap][Cap]x2 (purple)
Shield Array Mk XI [Cap]x2[Pla] (purple)

Fluid Dynamics
Antiproton Beam Array Mk XI [Acc][CrtH][Dmg] (purple)
Dual Antiproton Beam Bank Mk XI [Acc][CrtH][Dmg] (purple)
Antiproton Dual Cannons Mk XI [Acc][CrtH][Dmg] (purple)

Cold Call
Polarized Parabolic Deflector Mk XI (purple, Breen set)

Out In The Cold
Breen Transphasic Cluster Torpedo
Tricobalt Mine Launcher Mk XI [Dmg]x2
Tricobalt Torpedo Launcher Mk XI [Dmg]x2

Cold Comfort
Rapid Reload Transphasic Torpedo Launcher Mk XI (purple)

Cold Case
Supercooled Combat Impulse Engines Mk XI (purple, Breen set)

Cold Storage
Dielectric Oscillation Resilient Shields Mk XI (purple, Breen set)

Sphere of Influence
Omni-Directional Antiproton Beam Array [Acc][Dmg][Arc] (purple, Obelisk set)
Obelisk Subspace Rift Warp Core (purple, Obelisk set)
Antiproton Beam Array Mk XI [Acc]x2

A Step Between Stars
Solonae Deflector Array Mk XII (purple, Solonae set)
Solonae Hyper-Efficient Impulse Engines Mk XII (purple, Solonae set)
Solonae Resilient Shield Array Mk XII (purple, Solonae set)

Surface Tension
Console - Tactical - Counter-Command Multi-Circuit Energy Relay (purple, Counter-Command set)