The aforementioned Clip Show episode for the aforementioned reason.
"How's Bayou", well, sorta... There were two versions of the episode. The original was never completed, due to time constraints, but when the series was picked up for syndication, a second, more common version was shown with additional scenes and dialogue to keep the storyline in place, but with other dialogue taken out as well. Only the original was included on the DVD set, and the more common syndicated version is nowhere to be found in that set.
Almost all of the opening teasers save for the first episode and some season three episodes are gone in the DVD sets. Depending on who you ask, either they were not part of Shout! Factory's deal with DIC Entertainment, or they were accidentally destroyed by Disney during DiC's short tenure there.
Screwed by the Network: While NBC gave Captain N fair treatment for its first season, its second and third season became the target of network politics as NBC began to move away from its Saturday Morning block; NBC stopped promoting the series from season two onwards, meaning that viewers would have to rely on word-of-mouth in order to not miss a new episode, and the third season in particular was noted for the removal of many licensed characters (except those from Nintendo), shorter episode length, dialogue changes and shift to cheaper animation studios (the last of which was in favor for a superior performer, Saved by the Bell). NBC canceled the program without warning after this and season three's abysmal ratings (its pairing program, Super Mario World, also suffered this fate), and its timeslot was returned to the affiliates once the 1991-1992 television season ended. Its timeslot was later replaced by local news.
An issue of Nintendo Power during the show's run indicated that an actual game based on the cartoon was in the planning stages at one point. No doubt the sheer legal mess of using the various characters in one title killed this off fairly early on, however.