These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The zombie episode. It starts off with Jin and Mugen eating rare mushrooms, and ends with a nuclear explosion and the villain leaping out of his grave, and it is never mentioned again. The operative word here is mushroom.
The Baseball episode also counts.
Episode 9 may count as well, at least toward the end.
Complete Monster: Mukuro is the Evil Counterpart to resident Heroic Sociopath, Mugen. A particularly bloodthirsty pirate, Mukuro is first seen leading an attack on a ship for it's gold, killing the sailors onboard and shoving a lit grenade into the mouth of a subdued man who was begging for mercy. Through flashbacks it's revealed that Mukuro was the one who talked Mugen into piracy, and used him as muscle to kill the guards of a sugar shipment only to leave Mugen to die once he'd stolen the cargo. In present day we discover that Mukuro and his band slaughtered nearly an entire village, including the women and children. The only ones who were spared were the young men that could be used as muscle for his biggest heist yet: a raid on a government ship carrying 60,000 ryu in gold coins. He talks Mugen into joining up with him again, but it's only another set-up. Using his crew as canon fodder to lure the government security onto the pirate ship, Mukuro then uses a mass of explosives in an attempt to kill everyone, his own crew included just so he can keep the gold for himself. Mukuro also proves to care little for his "sister" Kohza, either, since he's spent his life controlling her, murdered her mother, and expresses an unreciprocated sexual interest in her. A sadist with a propensity for betraying everyone he knows and leaving no survivors from his attacks, Mukuro knows exactly what a bastard he is and relishes the darkness within his soul.
In the last episode, Jin and Mugen admit they consider each other friends.
In episode 24, Fuu is feeling melancholy because their journey is coming to an end. She leans into him and Jin puts a comforting hand on her shoulder.
Crowning Music of Awesome: The soundtrack, and with Nujabes' involvement, it's no surprise. There's also the haunting song that Sara sings as part of her traveling performer act and the one that plays over Mugen's flashbacks to his youth with Koza and Mukuro.
Ear Worm: Several. nujabes' "battlecry" (the opening theme), MINMI's "Shiki no Uta" (the closing theme), tsutchie's "pretending to…" and "sincerely", nujabes' "mystline" and FORCE OF NATURE's "vagrancy" are some select choices. Many Champloo fans have even stated that they thought the worst of hip hop music before this series came along and changed their minds about the entire genre.
Ensemble Darkhorse: Sara. Also, Yatsuha and Yukimaru make an appearance in a lot of fanfics for such a relatively small fandom. Probably for shipping reasons, but still...
Ho Yay: Actually played straight (no pun intended). The Dutchman comes from a sect who believes that enlightenment can be obtained through homosexuality. There's also the Jin/Yukimaru subtext, even though Jin has sex with women on multiple occasions and actually falls in love with a brothel worker in one episode. Mugen and Jin arguably count as Foe Yay.
Iron Woobie: Mugen. The Misguided Miscreants two-parter revealing his backstory gives him plenty of reasons to feel sorry for himself, on top of being betrayed by his childhood friend/possible love interest and nearly dying. But at any point does he let it get him down? No. He lets it make him angry. The man simply does not give a fuck.
Mugen: "I don't give a rat's ass about going to hell. I guess it's because I feel like I'm already there."
Nightmare Fuel: The zombie episode, especially the credit ending. Also, the way the counterfeiter was going to torture the secret police in episode 15. It involved molten gold and a funnel. Truth in Television in case you were wondering.
Superlative Dubbing: The English and French dubs have been very well received, the latter being considered the best French anime dub EVER, especially considering France's history of dubbing anime in general REALLY BADLY.