The first one who comes to mind is Artemis/Diana, a goddess who loved women, including Britomartis, Cyrene, Atalanta, and Anticleia. She loved the moon-goddess Dictynna (who is also identified with Britomartis) and the nymphs Daphne, Amethyst, Taygete, and Callisto. As Artemis Orthia, she was worshiped by both lesbian and gay devotees. As Artemis Pergaea, she was worshiped in hymns by the lesbian poet Damophyle of Pamphilia who led a circle of women loving women.
Greek mythology also includes the FTM story of Iphis and Ianthe, two women who fell in love: Iphis was transformed into a man and they got married.
Sappho invoked Aphrodite to win the love of a woman. Her Hymn to Aphrodite is the only complete poem of hers that survives. Her community of women worshiped Aphrodite and the three Graces. The goddess Aphrodite Anosia was celebrated by lesbian rites in Thessaly.
Helen was the name of a goddess worshiped at Argos and Sparta who was invoked for women's unions with women.
Pallas was the lover of Athena and even fused with her, the pair becoming known as Pallas Athena. Another nymph loved by Athena was Chariclo.
Sappho said Leto (goddess of night) and Niobe had been lovers before they became mothers. The Pleiades were associated with love between women in Sappho's poetry.
In Greco-Egyptian magical texts from Alexandria, the Erinyes were invoked for lesbian love spells.
The relationship between the goddesses Baubo and Demeter can be read as lesbian, likewise Ame no Uzume and Amaterasu.
In Hawaiian mythology the goddesses Hi'iaka and Hopoe were same-sex lovers. Hi'iaka had other goddess lovers, Omeo and Pauo-Palae.
The Hawaiian goddess Pu'uhele had a girlfriend named Puomaiai.
The Inuit goddess Sedna at the bottom of the sea has a female companion named Qailertetang.
The goddess Aurora was worshiped by Sappho's women on Lesbos and was the patron of same-sex unions of women. Another goddess named Aotis was worshiped by Spartan women loving priestesses like Agido and Hagesichora.
The Roman goddess Bona Dea was worshiped in a special women-only ceremony which was kept secret from men. Draw your own conclusions.
How about the story of Parvati and Malini... The two female deities loved one another and together conceived and became mothers to the god Ganesha. Malini was the servant of Parvati, she rubbed her body with scented powders and oils (this is a traditional Indian method of skincare), then when it came off her skin, she loved her so much instead of throwing it away she ate it and became pregnant with Ganesha.
The Hindu fire goddess Arani has been seen in lesbian terms, since in her ritual two pieces of wood are rubbed together to make fire, and both of them are given female names.
Diane Mariechild, author of Lesbian Sacred Sexuality, does a Buddhist tantric meditation during sex to experience her lover as the goddess Tara.
In Vodun, the lwa Erzulie Dantor is a patroness of lesbians.
In Cuba, the orisha Inle or Erinle is a patroness of lesbians and trans women.
Oshun is another orisha revered by lesbians. Audre Lorde's poem "The Winds of Orisha" has the lines "the beautiful Oshun and I lie down together / in the heat of her body truth my voice becomes stronger."
The Aztec goddesses Xochiquetzal and Tlazoteotl are protectors of patlaches, women who love women. Gloria Anzaldúa revived the word patlache. Chicana lesbian Cherrie Moraga has interpreted the Aztec moon goddess Coyolxauhqui as a lesbian deity.
In Feri, the Star Goddess and other deities contain all genders and sexual polarities within Herself, so might be understood as queer in all sorts of ways.
In 1989-1990, JoAnn Loulan took a survey of almost 600 lesbians and found that their favorite Goddess was Artemis/Diana, their second favorite was Aphrodite, and third favorite was Athena.
A great reference source in which I found some of the above examples: Cassell's Encyclopedia of Queer Myth, Symbol, and Spirit: Gay, Lesbian, Bisexual, and Transgender Lore (London, 1997).