I'm glad this has been helpful for people. I know we lost a few posts here, which is why I waited to continue this.
I added a "Possible influence" section for fun. I'll go back and add them to the other seasons if you guys like. It's just stuff that happened in the series and then was transfered to the comics. The idea could have possibly been from the series first, they're speculation then fact.
Here we go with Season 3
Episode 53-58
Loosely - Volume 2 #13
http://www.ninjaturtles.com/comics/m...me02/13/13.htm
Episode 59: Touch and Go
Raph segment - Challenges
http://www.ninjaturtles.com/comics/b...challenges.htm
Episode 60: Hunted
Tales Volume 1 #6
http://www.ninjaturtles.com/comics/m...ales/06/06.htm
Episode 61: H.A.T.E.
Volume 1 #12
http://www.ninjaturtles.com/comics/m...me01/12/12.htm
Episode 62: Nobody's Fool
Tales Volume 1 #2
http://www.ninjaturtles.com/comics/m...ales/02/02.htm
Episode 63: New Blood
New story
Episode 64: The Lesson
New story
Episode 65: The Christmas Aliens
Michaelangelo #1
http://www.ninjaturtles.com/comics/m.../mike/mike.htm
Episode 66: The Darkness Within
New story, possible influence for
Tales Volume 2 #45
http://www.ninjaturtles.com/comics/m...vol2/45/45.htm
Episode 67: Mission of Gravity
New story
Episode 68: The Entity Below
New story
Episode 69: Time Travails
Loosely
Volume 1 #8
http://www.ninjaturtles.com/comics/m...me01/08/08.htm
Episode 70: Hun on the Run
New story
Episode 71: Reality Check
Characters/Training room battle
Volume 4 #7
http://www.ninjaturtles.com/comics/m...me04/07/07.htm
Possible influence
Tales Volume 2 #47
http://www.ninjaturtles.com/comics/m...vol2/47/47.htm
Episode 72: Across the Universe
Characters - Planet Racers
Several issues none TMNT crossovers
Episode 73: Same As It Never Was
New story
Episode 74: The Real World Part One
Usagi Yojimbo Volume 2 #1-3
http://www.usagiyojimbo.com/casl/stories/green.html
http://www.usagiyojimbo.com/casl/stories/green-2.html
http://www.usagiyojimbo.com/casl/stories/green-3.html
Episode 75: The Real World Part Two
New story
Episode 76: Bishop's Gambit
New story
Episode 77: Exodus Part One
New story
Episode 78: Exodus Part Two
New story
Next, and last, Season 4!