Flying Circus is a skit show, while Goodies is a more of a regular half-hour comedy. While Circus had the luxury of deciding the length of any given skit; Goodies used a format that retained their basic characters throughout the show, as well as having a semi-coherent story running the length of each episode. This would plainly be harder to do and I think that is the reason why I think they may be better.

The Goodies also made 72 episodes versus Python's 45. Python's absurd humour is definitely funnier at its peaks but they were playing in a safer playground. Gilliam's art and animations also helped a lot in defining their uniqueness.

I watched The Goodies again a couple of years ago afraid that it would not live up to the memories. It did, and then some. Although I will admit to possible herbal enhancement ;)