The story that immediately pops into mind is the Kidnapping of Persephone. Hades takes Persephone, daughter of Zeus and Demeter (God of Agriculture), as his wife against the wills of Zeus and Demeter. Demeter falls into deep anger and brings famine across the world and will not relent until Persephone is returned. Hades relents, but not before tricking Persephone into eating a Pomegranate seed, forcing her to remain in the underworld. In a compromise, Zeus' mother said that Persephone will spend 6 months with Hades and 6 months with Demeter each year. This is the explanation story of the seasons. This easily falls under Morally Questionable.

The underworld having any kind of "evil" connotation was not present in Greek culture. After all, there was no heaven. Everyone goes to the underworld upon death. Virgil's Aeneid explores different tiers of the underworld where people would go depending on good or bad deeds, but Virgil was a a Roman author who came much later.

Another reason for any lack of evil deeds is that there just aren't that many myths about Hades in the first place. Even the few things he does that seem evil (kidnapping Persephone) are pretty tame compared to things done by other gods.

Artemis turned a man into a deer and had his own hunting dogs tear him apart because he saw her bathing.

Artemis and Apollo shot all 19 or so of Niobe's children to death because she bragged that having more children than Artemis and Apollo's mother made her superior.

Hera struck Tireseis blind because he favored Zeus' side when asked to settle an argument between them.

Hera has Ixion bound to a spinning wheel for all eternity in the underworld because he bragged about having sex with a cloud version of her.

A lot of myths involve gods being evil to humans. Hades actually comes out pretty nice looking simply by not being involved in many myths.

Hades in the original myths was seldom a major character, he was generally neutral though he would occasionally do stuff on behalf of other gods or occasionally demigods if they asked nicely. The only truly questionable act that he committed was taking Persephone by force though given how much the Greeks hated him its possible that the myth was altered to make Hades seem more villainous than he actually appears to be when he does show up in other myths. There is a theory that a lot of the myths we know about might actually have a bit of a bias towards Athena, the reason being that we really only know of the myths from Athens and not the other cities. Athena wasn't too fond of Poseidon or Ares hence why they are portrayed as bullies in the myths. Athena - or rather the people of Athens - didn't like Hades too much either. Hades appears to have been a bit too gloomy to be much fun around but the evidence points towards the god actually being quite docile, almost submissive compared to the other Olympians. He was helpful to Heracles, and wept along with Orpheus when the mortal came to him wailing and lamenting the death of his lover. He did kidnap Persephone but was rather kind to her and made sure she was comfortable. He seems to have had a bit of a bond with Hermes and was actually rather fond of Zeus.