List of which episodes focus on which turtles/characters
 

Similar to the sticky thread in the 4kids forum, I would hope we could get a similar plan for the OT (and Next Mutation), but let's not restrict it to just the turtles. I'll start with seasons 1 and 2 from the OT. Note that "All main teams" usually refers to the turtles, Splinter, April, Shredder, Krang (Dregg and Hi-Tech for Seasons 9 & 10), Bebop & Rocksteady.

Turtle Tracks- April
Enter The Shredder- Shredder
A Thing About Rats- Baxter
Hot Rodding Teenagers From Dimension X- Traag/Neutrinos
Shreddered and Splintered- Shredder/Krang
Return of the Shredder- Shredder
The Incredible Shrinking Turtles-Shredder
It Came From Beneath The Sewers- Leonardo
The Mean Machines-Raphael
Curse of the Evil Eye- Shredder/Baxter
The Case of the Killer Pizzas-Michelangelo
Enter: The Fly-Baxter
Invasion of the Punk Frogs-Shredder/Punk Frogs
Splinter No More- Splinter
New York's Shiniest- April/Rex-1
Teenagers From Dimension X- Neutrinos
The Catwoman From Channel 6- April
Return of the Technodrome- All main teams

Feel free to comment/discuss and add additions.

Sorry I put this on hiatus for so long, work has been hectic, here's some reference might help, I'll help you with the other characters too.
For the next several eps, Splinter becomes comatose in Beneath these streets, The turtles go on television with Clayton Kellerman in Turtles on Trial, then Irma grows tall in Attack of the 50-foot Irma, Donatello narrates with a Bogart impression in the Maltese Hamster, nobody really stands out in Sky Turtles, though Michaelangelo has a weight issue referenced at beginning and end, Shredder and Splinter get mind-switched in The Old Switcheroo, Burne and Vernon go off on a little investigation of their own in Burne's Blues, Zack makes his initial appearance in the Fifth Turtle, then the Rat king in Enter the Rat King, in the Turtles at the Earth's Core they make a new friend among the dinosaurs called Dippy the Diplodocus, April gets confused for a princess in April's Fool, then there's a robot from the future named MACC (Motor-Armored Computerized Combatant) in Attack of the Big MACC, the turtles go looking for a gift for Splinter which Shredder comes after and kidnaps Splinter with it in The Ninja Sword of Nowhere.

I've always thought David Wise did a really gutsy thing by making April the main character of the very first episode. Seriously, how many other shows of the era would fill the first five minutes or so of a show about anthropomorphic animals with a reporter in a yellow jumpsuit. She became the viewer's window into the strange world of the TMNT.