Savanti Romero, who would become one of the most powerful recurring foes the Turtles ever faced, started off as an assistant to Lord Simultaneous, a powerful wizard that controls the flow of time. Growing jealous of Simultaneous, Romero attempts to erase him from time. However, Simultaneous discovers Romero's treachery and transforms him into a goat demon before banishing him to 13th century Europe, where Romero takes over a village and makes it into his own fiefdom. Simultaneous's new assistant, Renet, accidentally teleports herself and the Turtles to Romero's village, where Romero manages to steals Simultaneous's time scepter from Renet. After the villagers rebel against Romero, Romero uses the scepter's power to create an army of the undead and orders them to slaughter the rebelling villagers. Simultaneous appears and banishes Romero to the Cretaceous period. Later, Romero appears, obsessed with revenge, and lures Renet and the Turtles to the Cretaceous period. After defeating Renet and the Turtles, Romero reveals his new plan: To sacrifice Renet as part of a spell that will cause the comet that wipes out the dinosaurs to miss Earth, causing humanity to cease to exist. The Turtles defeat Romero and he seems to have died, but he was merely frozen in time and reemerges in 12th century Japan. There, Romero attempts to build a new empire and plans to wipe out any Japanese clans that oppose him, which wipes out their ancestors in the present. The Turtles travel to medieval Japan and defeat Romero again. After a long absence, Romero appears again, traveling to limbo and planning to use an artifact called the Aga-Moo-Tou to make himself into a god and remake reality in his own image.
Skonk, from the September 1987 issue "Survivalists", is the leader of the far-right militia known as the "Committee to Rebuild American Patriotism". He felt that, because the Cold War didn't result in a nuclear war and his militia would not be able to prove their survival skills after such a event, he would try to start a nuclear war by setting off a nuke at a critical military facility. He and his militia kidnap a nuclear physics student from the University of Massachusetts and force him to create a crude nuclear bomb. The student escapes and bumps into the Turtles, warning them of the danger. Skonk kills the student with his sniper rifle. Thinking the Turtles are just people in costumes, Skonk orders his militia to kill all of them, not wanting there to be any witnesses to his plans. The Turtles easily defeat his militia underlings, so Skonk decides to return to his base and set off the nuke right away. When Splinter and Turtles try to reason with Skonk, saying he will kill countless people with his bomb, Skonk says he doesn't care, saying there are no innocents and everyone is guilty of allowing America to fall from greatness.
Dork Age: The "guest-writer" era that came from #22 all the way through #44. Although there were some well-received stories, for the most part the majority of them are considered a huge step down in quality, often portraying the book as Lighter and Softer and overly comedic (as noted by Bizarro Episode up above) rather than the dark action-adventure tone. Eventually Eastman and Laird themselves stated that only two issues from that era (#27-28) were canon.
Growing the Beard: As good as the comic and the franchise itself would later get, the original first issue which started it all was... underwhelming. The turtles all had the same one-note personality, the art was a bit shabby, and the Shredder was killed off in the first issue. Once that initial parody one-shot was turned into an ongoing series though, the creators realized that they needed to up their game. They weren't always successful at first though; with the Shredder already dead, where else was there to go? They tried throwing everything at the wall and seeing what stuck, but the comic still didn't have much of a voice other than just being kind of weird. On the other hand, they started developing the Turtles' personalities and gradually turned them into the characters we know and love today. By Issue 10, the Turtles had become fully fleshed out characters, and on top of that, they both brought back the Shredder and turned Casey Jones into a supporting character. From this point on, while the series would still delve into the weird and the strange, it had settled on being more of a serious action-adventure comic that occasionally ventured into Fantasy Kitchen Sink, and continued to develop the Turtles and their supporting cast further while actually letting the Shredder stick around long enough to be a proper threat. The comic finally earned the success it had gained, and it shows in the writing and the artwork, all of which was a major step up from that first issue. And that tenth issue was the moment where everything finally came together into both a cohesive and awesome whole.
Harsher in Hindsight: In Baxter's first appearance, he threatens to use his mousers to tear apart the structure of one of the buildings of the World Trade Center and make it collapse upon itself.
Moment of Awesome: The Turtles' first battle against the Foot Clan, humiliating the Shredder by easily killing his best troops, besting him in combat, and foiling his Taking You with Me attempt.
Also, that first comic in general, for far outperforming Eastman and Laird's idea of how much it would sell, and starting one of the biggest franchises of all time.
Signature Scene: Either the cover of the first issue, or the turtles leaping to attack the Purple Dragons in the two-page splash of the same issue.
Another one from Issue #1 is the battle against the Foot and the Shredder on the rooftop. Most incarnations since have had a battle against the Shredder that took place on a rooftop.
"Seinfeld" Is Unfunny: The amount of violence, especially in the early issues, were pretty shocking for the time, but considering how tame they are compared to several mainstream comics nowadays, newer readers may not be able to see why they made such a big deal.
What Do You Mean, It's Not for Kids?: No thanks to the 80s cartoon, which is far more well known. This comic could be mistaken for another child-friendly comic when it's not bloated with violence and gore.