i think it's only memorable because of the sheer level of repetition. The same music is in every episode and most of the music was in Isis, Ark II, Shazam, Space Academy, Scooby Doo, and even the animated Gilligan's Island. That music was ubiquitous in the early 70s.
Uhh,
Scooby-Doo was from Hanna-Barbera, not Filmation. Its music was by Hoyt Curtin, and not a single note of it came from the Filmation library created by Ray Ellis et al.
And while there was occasional overlap, generally Filmation's comedy series drew on a different set of library cues than their adventure shows did. With regard to
The New Adventures of Gilligan, you're probably thinking of the comedy cues that were used in episodes like "More Tribbles, More Troubles" and "The Practical Joker." But those were atypical for TAS.
Probably the show TAS shared the most cues with was
Lassie's Rescue Rangers, which was its immediate contemporary. Also the later SF-themed shows like
Space Academy and
Jason of Star Command reused a lot of their cues, and
Tarzan used a few as well. But the overlap wasn't as great as you suggest. Most every Filmation show featured a mix of original cues and generic library cues. Although the reuse of library cues diminished in later years; the 1979
Flash Gordon series featured a wholly new score (still recycled from episode to episode, but none of it taken from any earlier series).
As for the TAS theme, I've always loved it. I'm very fond of the orchestration. I don't think I ever considered it merely a knockoff of the original, since I'm pretty sure I discovered TAS only weeks after I discovered TOS. I saw my first TOS episode in January 1974, during the original run of TAS, and I think it was very soon thereafter that I discovered there was a cartoon version showing too.