Archenemies
Thunder Woman's biggest and most prominent villains, either because they are a particularly continuous threat to her, or because they figure into particularly significant events central to her character (and sometimes, both).
Apotheos
A 19th century British nobleman, adventurer, and archeologist with a bit of a god complex, and as the name implies is trying to achieve literal godhood, possibly with Samantha joining him to form a new pantheon. Poses a threat not just to her as a heroine, but to her very livelihood as an academic and archeologist thanks to being one of the largest donors to NPU and its board of directors, nevermind employing the rival diggers and mercenaries she sometimes has to deal with at international expeditions.
Dominus
An extraterrestrial risen from slavery to become a galactic conqueror, with a racial supremacist streak to him. Problem is, his supposed "master race" is dying off and sterile, and his scouts have identified Thunder Woman as possessing the possible means to reverse this trend. Naturally, this calls for a full blown invasion of Earth when smaller scale attempts to acquire her fail!
Helregin
Rival to Hera as Thunder Woman's primary archrival. Is a really long lived, enigmatic scientist whose conflicts with the heroine are initially little more than him being hired to help other criminals fight back against her, but over time becomes a bit more personal, as when he kidnaps her best friend and turns her into his minion. He seems to be obsessed with the source of her divine powers, which he believes are key to his research into the creation of life.
Hera
While time has tempered some of the more extreme traits of the Hellenistic deities, in Hera's case it's only amplified them. And when Samantha arrives at just the right time to completely undo Hera's plan to supplant the Dodekatheon with her own "Heratheon" and then return to Earth to bring it to heel, she naturally declares the hapless human enemy number one. It's basically Hera's almost relentless onslaught of attacks and schemes that causes Samantha to become Thunder Woman in the first place, and the mad goddess is also responsible for multiple members of the heroine's rogues gallery. Even Apotheos, Helregin, Miranda Iryn, and Nemo Oudeis' presence as some of TW's greatest enemies are all indirect consequences of various actions by Hera.
The Infernal Empress
A hugely powerful, primordial entity that takes the form of a demonic woman. One of the oldest beings in all reality, she controls the literal center of all existence, a group of realities known as the Infernal Realms that encompass all possible hellish, dark, and cthonic realms. Despite this she is not strictly malicious in her encounters with Thunder Woman, appearing to play at some larger, greater game with the heroine that these skirmishes form a part of.
Miranda Iryn
One of the wealthiest, most powerful people on Earth. Initially she seems to come to Newport to clean up the mess left by Derek Duvall's horrific handling of incidents involving attacking Thunder Woman and being exposed for numerous illegal activities, but in truth targets Thunder Woman specifically as part of a plan with a secret government organization that somehow involves Olympus and the Dodekatheon itself.
Nemo Oudeis
The leader of a superhuman mercenary and human trafficking outfit turn host for a primordial nihilistic force imprisoned in this reality by the Dodekatheon and Zeus in particular. After initial encounters with TW he sets off a series of events that coincide with both Miranada Iryn and the Children of Ares' separate schemes against the heroine, culminating in him annihilating an entire borough of Newport, the lowest low point of her career.