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.
Broken Aesop: all over the place, but not as many as you would think considering the nature of this show.
Despite espousing (repeatedly) that everyone should be themselves and beauty is on the inside, Hercules only has love affairs with beautiful women. To his credit, Herc only goes for people he falls in love with (and has rejected the likes of King Thespian's Daughters). Still, it's all off-putting compared to the moral of "Protean Challenge" or such.
There were a number of episodes where the moral was essentially "war bad" or "murder bad", but fundamentally both Hercules and Iaolus make their living as warriors, and they essentially never actually check a given monster to see if it's sentient before ganking it.
It helps that, as a camp comedy show, when one writer contradicted another it was usually lampshaded, and there are a number of episodes specifically pointing out the failure of other episodes, such as the introduction of Typhon and the explicit acknowledgement that Echidna's hatred of Hercules is pretty much entirely justified, since he murdered all of her children before the beginning of the series. There is also some evidence that the changes are actual personal growth (he stops hiring on to wars as the first three seasons progress) rather than hypocrisy.
Darphus from season one's "The Gauntlet" and "Unchained Heart" (as well as an Alternate Continuity in Part 2 of season 4's "Armageddon Now) is the former second in command of Xena before her Heel-Face Turn. Darphus earns Xena's disfavor by sacking innocent villages and slaughtering women and children for fun. When Xena objects, Darphus stages a coup on her after trying to force her to murder a baby. When Xena survives the gauntlet to leave the army, Darphus tries to have her killed anyways. After being killed by Xena, Darphus is revived by Ares and carries on a brutal campaign of slaughter where he also has care of Ares' monstrous pet. Darphus feeds innocent victims to said monster and shows no hesitation in killing his own men as well just for displeasing him.
Mayhem from season 4’s "Prodigal Sister" is the leader of a renegade band of Amazons that routinely terrorizes the countryside in Greece and massacres entire villages, except for the little girls she turns into her weapons. Most Amazons who did raids would go for minimal loss of life, and are appalled by Mayhem's actions. She personally blinds Ruun, (just after killing his parents and kidnapping his sister who she turns into a mindless killing machine) who's only five years old. Fast forward years later, when most of the renegade Amazons have rejoined the Amazonian Nation, Mayhem still leads raids which Rape, Pillage, and Burn entire villages for fun. When confronted by Hercules, she laughs off that her actions will lead to an Amazon Civil War which will be crushed by the outside world. And finally, when confronted on what she did to Ruun and his sister Siri after she is beaten by Hercules she flat out says "So what, I turned her into the greatest Amazonian Warrior!"
Xena, who got popular enough to her own spinoff series that actually surpassed this on in popularity.
Growing the Beard: The fifth season brought a more serialized (and at points, darker) approach to storytelling than previously, as well as giving the main cast members wider acting opportunities. The season also benefited from Kevin Sorbo having fully recovered from medical problems that prompted lessened roles the previous season. Both Sorbo and Hurst have spoken highly of Season 5, citing the energy that Kurtzman and Orci brought in as showrunners.
Harsher in Hindsight: In the Amazon Women TV-Movie, while talking about Iolaus' impending wedding, Hercules off-handedly brags that he might get a wife or two himself one day. His two marriages ended very badly, and he did not take any of that well.
Hilarious in Hindsight: In "Les Contemptibles," Michael Hurst's French character suggests calling their La Résistance group "the Powerful Rangers." When Power Rangers production was moved down to New Zealand, a number of local Hercules/Xena actors obtained various roles, including Michael "Vexacus" Hurst himself.
In "Porkules," Autolycus argues with a talkative, intelligent parrot. Became kind of a staple of another series starring Campbell.
Hercules and Iolaus are pretty damn prominent in the Ho Yay department without the fanfic. For example, every time Iolaus dies, Hercules is at first grief-stricken (insert Big "NO!") and then he immediately goes to whatever Underworld is nearest to get him back. Iolaus' death in season 5 puts him in the biggest Heroic BSODever, with him not eating, sleeping or shaving for 3 days, and then him getting angry at the fact that Nebula and Iolaus were together and that her grief isn't as great as his, and then, after failing to get him back from the Underworld, he gives up helping people entirely and takes Nebula's ship for a suicide run into a storm screaming "I don't care anymore!" The fact that Iolaus' death is more damaging and painful for Herc than the deaths of both Serena and his own family, moving him to nigh suicidal depression and making him say that he never wants to go back to Greece again is pretty damn suspicious.
And then, when Dahak traps Iolaus inside his own dead body and won't let him move on, he comes to try to seduce him into opening his heart to him. First he tries the form of Iolaus' father to try to make Iolaus think he is in the Elesian fields. And then he tries a number of forms to appeal to him. First he tries Nebula with "is this what you want, lover?" And then tries Hercules, which he stays in. The entire sequence is so full of subtext that even writers of Xena would be applauding. YMMV whether you consider Hercules going inside Iolauswhen he's trying to exorcise Dahak means anything.
Afterwards, when Herc takes Iolaus' double to Iolaus' grave (yeah, bringing Iolaus' double back from another universe in order to partner up with him doesn't look suspicious...), Iolaus' double says "I'll leave you to spend some time alone with him" and Herc says "I've had hundreds of those." However you interpret that, it at the very least means he has come back to Iolaus' grave a ridiculous number of times.
Even in the earlier, campy series, there are constant references to how close they are. They are always "partners", each "part of each other", and even at one point when Iolaus goes off for a quick one-night stand with a sex friend of his, Aphrodite quips "what, you and Herc don't do that for each other?" with both of them just smiling knowingly. Even Iolaus' long list of short one-night-stands with women but never any real relationships looks suspicious (and Hercules has no casual sex whatsoever, and no real relationships until after Iolaus is dead and he's grieved).
Then there's this in season 4:
Nebula: Quite a firm handshake between you two.
Iolaus: Yeah, so?
Nebula: So I think it's great.
Iolaus: Well I'm glad you approve.
Nebula: Yeah. So, how long you two've been together?
Herc will not kill anyone, however he will also condemn anyone who chooses to kill (except in battle). E.g. in one episode, the sole sheriff of a town is about to die (he has one day left). His town is over-run with gangs of cold-blooded killers and thugs (guys who kill and torture defenseless men, women and children indiscriminately and loudly boast about past crimes and plan new murders in public) who he takes to court, but everyone is too scared to testify or to convict them (when they should have been hung long ago). This man is the only one who who stands up to these thugs, and he has a new-born son with no relatives that he knows he won't be there to protect him. So he goes out and kills these men so they can't kill anyone else. Despite the fact that if justice would have had its way, these men would have been dead by hanging long ago - and this sheriff was the one who took all these men to court in order to be punished by hanging - Hercules calls his act "evil" and Celestia - the messenger of Death - agrees with him. This isn't "these people did not have a fair trial to decide their innocence", these men were clearly guilty and would have been convicted for any one of their numerous crimes, and the sheriff is now 'doing evil acts that must be stopped' (as Hercules says).
In fairness, Hercules moralizes loudly while the sheriff is going after actual murderers and rapists, but doesn't actually try to _stop_ the guy until it's turned into a full-on rampage and he's about to start executing teenagers for being insubordinate and engaging in petty crime.
Herc goes to ridiculous lengths to Save the Villain, in many episodes. However, for people like Xena and Dirce, he lets them go, despite their manifold crimes, as long as they promise to stop, while for many people who have done much lesser crimes, he forces them to "face justice" even though they have accepted the error of their ways and want to atone. Basically it works like this: killed manifold people in cold blood, conquered entire countries, oppressed people's way of life and sold people into slavery = freedom; performed many robberies, became part of a gang with a bad reputation, killed a couple of people in cold blood = death by hanging (according to justice). And the times that Hercules thinks that the court is unfair, he will free people or stop the court from performing punishments (despite the fact that the point of justice by court is that a magistrate or group of people decide according to their interpretation of the law and the crime). So it boils down to: Hercules decides someone's fate (including delivering them to a court knowing they will be killed), and then allows the court to kill the people that deserve it rather than by his own hand, because he doesn't believe in killing.
Possibly Intentional Values Dissonance — in the bronze age, killing your neighbor or stealing his cow was a terrible crime, but getting twenty of your buddies together and conquering the next town to kill them and take their cows was politics as usual.
Actually lampshaded in an episode where he lands in 'enlightened' (read: anachronistically liberal and modern) Athens and is immediately put on trial for, essentially, being a vigilante rather than following the law. He's called out very specifically on giving Xena and another former assassin/mercenary a free pass while killing others that did far less.
Moral Event Horizon: The murder of Hercules' family was this for Hera. Before, their antagonistic relationship was more like business as usual. Afterwards, it became personal.
As far as Hercules is concerned, Zeus arguably has two of these - 1) for not stopping what happened to Herc's family (he was having an affair at the time), and later 2) for not stopping Serena from being killed. Both cases involved members of Zeus' pantheon waging a war on Hercules and Zeus not keeping them in line despite opposing what they do.
Special Effects Failure: Some of the earlier CGI and blue screen effects have not aged well. (To be fair, the budget wasn't exactly high.) Hilariously, this was referenced in "For Those of You Just Joining Us":
Ares: What about those cheesy blue screen effects? They look so fake.
Strawman Has a Point: Hercules often chastises people for their sacrifices and blind worship, telling them that the Olympians don't care about their suffering and won't help them regardless of what they do. He's usually right in that regard, but sometimes he's faced with everyday, good people that aren't lucky enough to be half-god. From Circle of Fire:
"It's easy for you to go around disrespecting the gods! There'll always be a place at the table for you up on Mount Olympus, but we're at the gods' mercy! Our faith, our sacrifices is all that stand between us and death!"
Tear Jerker: In the season 3 episode The Lady and the Dragon, the villain of the week (Adamis) uses a dragon named Braxis to do his bidding. However, as we later find out, Braxis is only a child who's still mourning his mother's death. Even worse, Adamis lied to him and said Hercules had killer her when Adamis was actually responsible. Adamis even plans to kill Braxis because he's getting too big to control, even though Adamis has actually grown fond of him.
They Wasted a Perfectly Good Plot: A late episode has Zeus raise Hercules to full godhood after the death of his mother. When Hercules finally confronts him over some odd behavior Zeus admits that he did this because he wanted Hercules to protect him from the other gods. After Hera is banished to Tartarus this plot point is never brought up again and we never see much to suggest that the other gods are considering getting rid of him.
I don't think it would be a problem afterwords. It would take all the gods including Hera to confidently overthrow Zeus. She was one of the most powerful so without her they did not have the raw power. Her getting thrown into Tartarus would have scared the others into falling back in line. Finally, the gods quarrel with each other as Zeus. Without a strong leader to unite them they could not get their act together to do anything to Hera.