Entire run of the second doctor portrayed by Patrick Troughton, 119 episodes of which 61 are reconstructions and 2 are animations. 

It's unfortunate that so many episodes of the 2nd doctor's stories were junked but the reconstructions give a good representation of what they would've been like. The fan reconstructions (uploaded by JohnnyFanboy) have linking narration between the dialogue whereas the loose cannon reconstructions (uploaded by Eldoctorio) have subtitles, all have a resolution of 640x480 with clean soundtracks.

I was able to get the Lost in Time boxset, so the episodes from these partially missing serials are my own DVD rips: 
The Underwater Menace (Part 3), The Moonbase (Part 2 and 4), The Faceless ones (Part 1 and 3), The Evil of the Daleks (Part 2), The abominable Snowmen (Part 2), The Enemy of the World (Part 3), The Web of Fear (Part 1), The Wheel of Space (Part 3 and 6), The Space Pirates (Part 2). 

All the DVD rips have the following specs:
Video: Container - MKV, Codec - h264 @ 872 kbps, Resolution - 640x480 (4:3 aspect ratio)
Audio: AAC @ 128 kbps

0403 - The Power of the Daleks - Fan Reconstruction
0404 - The Highlanders - Fan Reconstruction
0405 - The Underwater Menace - Reconstruction by Loose Cannon. Part 2 has been recently found, but it hasn't been released on DVD yet. 
0406 - The Moonbase - Reconstruction by Loose Cannon
0407 - The Macra Terror - Reconstruction by Loose Cannon, 
0408 - The Faceless Ones - Reconstruction by Loose Cannon
0409 - The Evil of the Daleks - Reconstruction by Loose Cannon
0501 - The Tomb Of The Cybermen - DVD rip
0502 - The Abominable Snowmen - Reconstruction by Loose Cannon
0503 - The Ice Warriors - Reconstruction by Loose Cannon (Part 2 and 3), rest are DVD rips.
0504 - The Enemy of the World - Reconstruction by Loose Cannon
0505 - The Web of Fear - Reconstruction by Loose Cannon
0506 - Fury from the Deep - Reconstruction by Loose Cannon
0507 - The Wheel In Space - Reconstruction by Loose Cannon
0601 - The Dominator - Australian digital broadcast (ripped by 1512).
0602 - The Mind Robber - DVD rip
0603 - The Invasion - DVD rip, parts 1 and 4 are animations created Cosgrove Hall to replace the lost episodes. One other serial from the Hartnell era (Reign of terror) also received this treatment as will the two missing episodes from The Ice Warriors. 
0604 - The Krotons - VHS rip.
0605 - The Seeds of Death - DVD Rip 
0606 - The Space Pirates - Reconstruction by Loose Cannon
0607 - The War Games - DVD Rip