The Mike Skully years (seasons 9-12) were for me the low point of the series, although individual episodes were very good and even then, compared to other contemporary shows, it's still a pretty good animated half-hour or so. Certainly the infamous "Homer gets raped by a panda" episode wasn't nearly as bad as I remembered it, but it was definitely not among the best episodes from that period.
Having seen some of the episodes after that period (when Al Jean became showrunner again) I actually started to like it again - can't really place a finger on it, but it seemed to be from the middle of season 13 onwards. However, it was becoming somewhat gimmicky at times, with heavy reliance on guest stars to lift the episode.
For me, the show really became brilliant from the middle of season 2 onwards - "Bart the Daredevil" for me was the tipping point, the moment the show jumped the gorge. (Funnily enough, that episode featured a character jumping a gorge.
) That season we were also treated to gems like "Lisa's Substitute", and then onto seasons 3 and 4 which were just perfect.
"Lisa's Wedding" from season 6 is still my all-time favourite episode. "I get me brain medicine from the Nartional 'Ealth!"