There are a lot of names that can work for witches, including most of the Goth Names and almost any herb or crystal names, but I decided (mostly for my own reference) to compile a list of names that are particularly good for witches, enchantresses, sorceresses, etc. that may be good or evil. Once again, I may have heavily drawn on mythology! I'm also leaving most crystal names (Amethyst, Carnelian, etc.) off of it because any of them could work. The first list is all female names. I haven't found nearly as many male names.
Acrasia: A witch in The Faerie Queene who tempts and bewitches people, controlling their minds. Means "lacking command."
Agatha: Means "good." A disproportionately common name for witches in media. (For example, the Enchantress in the live-action Beauty and the Beast, Aggie Cromwell from Halloweentown, and Agatha Prenderghast from ParaNorman).
Akantha: A Greek name meaning "thorn."
Alcina: An evil sorceress and seductress from Orlando furioso, and the title character of a series of operas. Meaning uncertain.
Aradia: The title character of Charles Geoffrey Leland's book Aradia, or the Gospel of the Witches. A moon goddess and basically the witch version of Jesus, at least in that book.
Arcana: Latin word meaning "secret" (literally "to shut in a chest"), also a word for the two groups of cards in a tarot deck.
Argante: The Queen of Avalon in one Arthurian text, a version of Morgan le Fay. Might be related to argenta ("silver").
Arianrhod: A Welsh goddess, associated with the moon, stars, fertility, and the passage of time. Means "silver wheel."
Armida: The name of the witch/seductress in Tasso's Jerusalem Delivered, meaning uncertain.
Asterope: The mother of Circe. Means "lightning."
Autumn: The season containing Halloween/Samhain.
Belladonna: A poisonous herb. Means "beautiful woman."
Briar: Refers to thorny bushes. Could be associated with evil enchantments, beautiful roses, or both.
Brigid: Celtic fire goddess. Means either "strength, virtue" or "exalted one."
Cassandra: A Greek prophetess whom Apollo cursed so no one would believe her. Means "she who entangles men." Could be shortened to "Cassie."
Cerridwen: Welsh enchantress goddess associated with the sacred cauldron of divine inspiration. Means "blessed woman."
Circe: A sorceress in Greek mythology who turned men into animals and who was a priestess of Hecate. Means "hoop-round."
Despoina: A daughter of Demeter and Poseidon associated with Arcadian mystery cults. Means "the mistress."
Diana: Roman name of the goddess Artemis, the virgin goddess of the moon and the hunt. Associated with Dianic Wicca, a modern cult centered around this goddess.
Edana: Means "little fire."
Elergia/Annowre: An evil sorceress in Arthurian legend who tries to seduce Arthur.
Endora: The Witch of Endor was a sorceress in the Bible.
Empusa: Female monsters that served Hecate.
Esmeralda: The name of Granny Weatherwax (from Discworld), means "emerald."
Freya: Norse goddess of love, beauty, sex, and war, means "lady."
Ganeida: An Arthurian sorceress, a sister of Merlin.
Grimhilda: The name given to the Evil Queen in Disney's Snow White. Good for fairy-tale-esque witches, could also work for a kinda Gothy heroic character.
Gwendolyn: A Welsh name meaning "white bow" or "white ring."
Habundia: "Abundance," a name for the queen of witches or fairies, associated with Diana, Mab, Nicnevin, and Hecate. (Also the name of a benevolent fairy godmother in one of the earliest modern fantasy novels.)
Hazel: Witch-hazel is a shrub with yellow flowers, associated with witches because of its name and its medicinal properties.
Hecate: The goddess of witchcraft and the crossroads in Greek mythology. Means "worker from afar."
Hecuba: The Queen of Troy, mother of Cassandra. Uncertain etymology, possibly related to "Hecate."
Hellawes: An evil sorceress in Arthurian legend who seeks to kill Lancelot so she can embalm his corpse and kiss it every day to spite Guinevere. Creepy.
Hellebore: A poisonous herb.
Ianira: A name of several nymphs in Greek mythology, possibly meaning "enchantress."
Ingrid: A Norse name combining the name of a fertility god and the word for "beautiful."
Ivy: A plant thought to drive out evil spirits.
Lamia: A vampire-like monster from Greek mythology that eats children. Name of the witch in the film version of Stardust.
Lilith: The Queen of Demons in Hebrew folklore, means "of the night" or "screech owl."
Lilura: Basque name meaning "enchantment."
Louhi: An evil witch queen in Finnish mythology. Means "trance."
Luna: Roman goddess of the moon.
Maeve: Based on Irish Gaelic, means "intoxicating." Possibly related to Queen Mab.
Medea: Means "cunning," a sorceress in Greek mythology who helped Jason steal the Golden Fleece. Took violent revenge when he left her for another woman.
Melissa: An apprentice of Merlin, who rescues the victims of Alcina. Means "honeybee."
Morana/Marzanna: The Slavic goddess of death and winter, means "death."
Morgana: Name of the famous sorceress Morgan le Fay from Arthurian legend. Means "sea circle."
Morrigan: Irish goddess of death, war, and ravens, means "great queen."
Morwenna: A Welsh name meaning "maiden," the name of the witch in the book version of Stardust.
Nepenthe: A magical drug from the Odyssey that cures sorrow and causes forgetfulness.
Nicnevan: Queen of the Fairies in Scottish folklore, and the witch queen of Samhain. Means "daughter of the divine." Identified with Hecate.
Nimue: A name for the Lady of the Lake, and/or the sorceress who encased Merlin in a tree with his own magic. Means "memory."
Nyx: The Greek primordial goddess of and personification of the night.
Orenda: Iriquois name meaning "magical power."
Persephone: Greek goddess of flowers and Queen of the Underworld. Means either "wheat-thresher" or alternatively "destroyer."
Raven: The bird, associated with death, magic, and prophecy in multiple mythologies.
Selene: The Greek goddess and personification of the moon.
Strega/Striga: "Strega" is the Italian word for witch (and a word for Italian neopaganism). "Striga" is the Latin word for witch and means "screech owl" (owls are in the order "strigiforms") and a genus of flower called "witchweed."
Taika: Finnish, "magic spell."
Vervain: An herb with magical and medicinal properties.
Vivian: A name for the Lady of the Lake, means "lively."
Willow: A tree associated with witches and spirits.
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Male Witch Names
Abdecian: Means "to get by asking," as in a magic spell. (I actually have no idea what my source for this is, and have not been able to find it again, so take with a grain of salt.)
Alaric: Germanic, "all-powerful."
Amergin: A druid in Irish mythology, "born of song."
Aspen: A white tree, associated with fairies. Its leaves turn golden in the fall, and they appear to "shimmer" in the breeze.
Aurelius: Latin, "golden."
Briar: Refers to thorny bushes. Same fairy-tale associations.
Gwydion: Means "born of trees," a magician and trickster god in Welsh mythology.
Hemlock: A poisonous herb used in spells.
Hunter: Self-explanatory. Modern witchcraft tends to involve the worship of forest gods associated with hunting.
Mabon: Welsh, "divine son," a figure in Arthurian legend. His name was given to the autumn equinox in modern paganism.
Maddock: Welsh, "fortunate."
Melchior: One of the Biblical magi, "king of light."
Raven: The bird, associated with death, magic, and prophecy in multiple mythologies.
Rowan: Irish, "little red one," the name of a tree with the ability to ward of evil.
Taliesin: A legendary bard in Welsh folklore, the son of Cerridwen. Means "shining brow."
Valerian: A medicinal herb. "Health, vitality."