Rurouni Kenshin did that, but from what I can remeraber, compared to other long running shonen series there weren't that many moments where characters looked down-right hideous. Kenshin and Shishio's first encounter and then Kenshin vs Hiko (Aoshi vs that old man.. I can't think of his name for nothing) are some moments that really stuck out. It's a good thing those fights were good (or interesting).
Yu Yu Hakusho seems to be one of those rarities for me. I don't know if it seemed like this to anyone else, but to me it seemed like with each passing arc/saga the character models were improving. Honestly, I thought it started out with poor artwork and gradually builded up, and looked really good by the time it all came to an end, despite the colors looking very bland.
And then there's Ghost in the Shell: SAC. (best series ever) Let's not get it twisted. I don't think there was ever anything wrong with the models or animation (I compare everything to this). But there were some episodes (by some I mean like 2 or 3) where you can tell it was either drawn by another team or someone had a lazy day. (And even on their lazy days the models still came out to look really good) Like I said, I don't think they were bad, but you can notice it though, that's all I'm saying.
And then there's, of course, Bleach and Naruto (No where near my favorites). Even during the canon parts they've had some horrible moments. (DBZ as well, but I don't know what's real and what's not, but don't care at this point either) It's been a while since I've seen both (I think about 2 months) so I don't know if either one has improved or not.