Awesome, Dear Boy: Tim Daly said the reason he signed on to do Superman's voice in this series was because he thought it would be fun to play a superhero in a superhero cartoon. He later said he underestimated just how difficult voice acting for a superhero, especially one of Superman's stature, would be.
Although they all praise the performance of the voice-actors (especially Jimmy Olsen's VA, David Kaufman), the production team has a very low opinion of "Superman's Pal", an episode of the third season focusing heavily on Jimmy Olsen.
They have a low opinion of "Little Big Head Man", which they felt tried and failed to recapture the success of the earlier Mxyzptlk episode.
Executive Meddling: Originally, Ma and Pa Kent were supposed to die in Apokolips... Now!, but DC said that if they were killed they would need to be brought back to life later. Unwilling to walk down that path, the target was shifted to a different character.
Off Model: The animation team did this intentionally, removing the "S" shield from Superman's cape in order to save themselves from having to animate how the shield would look as the cape rippled and moved.
The original, much darker plans for "Little Girl Lost" involved Superman discovering that Darkseid was turning humans into Parademons, with heavy Nazi overtones for the transformation camps, and the episode ended in the midst of a large scale battle on Apokolips. The authors do like the finished episode, but were very disappointed with the heavy backtracking after they had already been given the go-ahead for the initial plot.
"Legacy" was intended to kick off a season's worth of episodes about Superman regaining the world's trust. However, a pushback and other projects (Batman Beyond) led to it being produced as the finale instead, while the theme of public distrust for metahumans became an underlying plot thread in Justice League.
Clancy Brown originally auditioned for the role of Superman before being cast as Lex Luthor, and according to the producers his initial reaction to being asked to play Luthor instead was "Am I ever gonna get to play a good guy?"
Sherman Howard was considered for the role of Luthor, having previously played the character in "The Adventures of Superboy". According to Bruce Timm, Howard gave an impressive audition, and was nearly offered the role . . . until Clancy Brown walked in. Howard gave one-off performances as The Preserver and General Steppenwolf, and later voiced the Luthor-like Derek Powers in Batman Beyond.
Paul Dini and Bruce Timm originally wanted to use Kara Zor-El as Supergirl, but they were denied by DC Comics due to the then-current "Superman is the only survivor of Krypton" edict. Although they went as close as they could get, with Kara being Clark's adopted cousin and from Krypton's "sister planet", Argo (a Mythology Gag to that side of the House of El living in Argo City in the comics), essentially making her as close to Kryptonian as possible. An additional Mythology Gag is her family name - Kara Zor-El's mother was named Allura In-Ze, with said surname given to the show's interpretation of Kara.
Lex's robotic Tyrannosaurus rex was going to be given by Superman to Batman. This would have explained its appearance in the Batcave.
The original ending to "A Little Piece of Home" would have also included Superman giving the piece of kryptonite from the episode to Batman for safe keeping.
There were some art sketches of girls for the strip bar scene in World's Finest. They wore nothing but black bikinis and long black leather boots. The final cut of the episode had the girls in flirty dresses instead.
There were some thoughts of having Captain Marvel/Shazam appear in the series, possibly in a episode that would also introduce the Justice League, but a combination of rights issues and not wanting to introduce the Justice League out of nowhere put an end to it.