flame of recca- the tournament finals, I felt the whole tourney thing was a ripoff of yu yu hakusho, then it ended all anti-climatic(kaoru didnt even fight after learning the kougan ankis newest form.) kurei and recca team up and its stupid. the manga goes way further (I thint the tourney ends in volume 14 out of 33) but I havent gotten to it.
The anime REALLY messed up in the tournament finals, because by then their budget was pretty much exhausted (which is why they didn't animate Joker vs. Kaoru). Joker vs. Kaoru was in the manga, and it was an awesome fight. The fight between Recca and Kurei was lame as well, because they cut it short and didn't use a lot of the awesome things the manga had (Kurei using Jisho, Recca destroying the arena with Kokuu + Nadare, their brawl when they exhausted their flames). And finally, the thing about Kurei's clone…. that was really retarded and thrown in out of nowhere. Though, Mori Kouran DOES make a clone of Kurei that's capable of using his flame, but it's nothing like that...
I'd heavily recommend that you read the manga, because the anime goofs up a lot of cool moments and leaves a lot of things out. And yes, the manga goes way beyond the tournament. There's a bit of a slump after the tournament where they go into the Hokage Sealed Cave, but the saga after that (the SODOM Arc, the climax) is the most badass part of the manga.
Jumping the shark? Well, for me...
Naruto: Maybe somewhere during the Tsunade arc, I remember heavily losing interest when Naruto spent 50 chapters training his rasengan. But then, there was a battle royale between Orochimaru, Tsunade, and Jiraiya so that was OK. Immediately after that, when Sasuke beats up Sakura and leaves, I'm like "OK, this is gay."
Kenshin: I don't think it ever jumped, but there's a few point where it's in a slump. The Kyoto Arc was its pinnacle, but I don't think the Jinchu arc was at all bad. Pretty awesome as far as I can tell so far.
Fullmetal Alchemist (anime): AL BECOMES THE PHILOSOPHER'S STONE, OOOOOOO. Stupid plot twists ahoy.
Bleach: Somewhere in the Soul Society the manga really lost its way. Hopefully it'll regain what it once had in the upcoming arcs.
Dragonball: Goku being an alien, yes. Like Bucc said, it still had good moments, but...