Disclaimer: This is still an incomplete list. There are still a number of deities that I have not listed yet. If more information has been posted on a deity, there will be a link to the corresponding thread.

Aabit: a singing Goddess
Aah: a moon God
Aker: an earth God shown as two heads or two lions facing in opposite directions (east and west). Said to absorb poison from your body when called upon.
Amen: a sun God
Ami: a fire God
Ami Neter: a singing God
Ami Pe: a lion God
Amu: a dawn God
Amun: creator god, worshipped at Thebes as King of the Gods
Amutnen: a Goddess of milk cows
Anpu(Yinepu, Anubis): jackal God, inventor or mummification and guardian of cemeteries
Apet: a mother Goddes, nursing mother
Apuat(Upuat): a white or grey jackal god who guides souls to their place of rest
Aput: a messenger God
Asar(Wesir, Osiris): Ruler of the underworld and God of crop fertility
Asbit(Asbet): a fire Goddess
Aseb: a fire God
Aset(Isis): widow of Asar, mother of Heru and Mistress of Magic
Ashket: a Goddess of the winds
Ashu: water God
Aua: God of gifts
Auit: Goddess of nurses and children
Bait: Goddess of the soul
Baket: a hawk Goddess
Bast(et): the extra -et is silent. Feline Goddess, defender of Ra and bestowed of fertility
Bat: Predynastic Goddess of cows, the sky and fertility
Bata: God of war and the chase
Bekhkhit(Bekhkhet): Goddess of dawn's light
Bes: protector God
Djehuty(Djehuti, Tehuti, Thoth): lunar God of wisdom, language, and writing, with ibis and baboon forms
Geb: earth God, consort of Nut and head of the divine tribunal
Hapi: God of the Nile and fertility.
Heh: God of infinity, represented a wish to live for thousands of years
Heka(Hike): God of magical speech
Hekat(Heqet): Goddess of childbirth and protection, symbolized by a frog
Henkheses: God of the east wind
Heru, sa Aset(Horus, son of Isis): sky falcon, opponent of Set and archetypical ruler of Kemet
Heru Ur(Her-Wer, Horus the Elder): a sky God and Set's "opposite"
Hesa: a singing God
Hwt-Hwr((pr. Hoot Hoor))(Het Heru, Het Heret, Hathor): cow goddess of birth, death, and cosmic renewal
Hu: the God of Authoritative Utterance/Command
Hutchai: God of the west wind
Kekui(Keku): the God of the hour before dawn, "Bringer in of the light"
Kekuit: Goddess of the hour after sunset, "Bringer in of the night"
Khephera(Khepri, Khoprer, Xepera): a sun God, usually associated with the rising sun
Khnum: ram God, creator god and controller of the Nile flood
Khonsu: creator moon God and controller of Fate
Khurab: a bird Goddess
Ma'at: Goddess of truth and order
Maa: God of sight
Mafdet: a lynx Goddess
Mahes: a lion God
Mathet: tree Goddess, said to help the deceased climb into heaven
Merseger: a cobra Goddess, said to live on a specific mountain in Kemet
Mesen: a blacksmith God
Meskhenet: the Goddess that presides at childbirth, symbolized by a birth brick
Min: God of male sexuality and agricultural fertility
Montu(Monthu, Menthu): war God, falcon headed, also represented by a griffin
Mut: avenging Goddess worshipped at Thebes as consort of Amun and mother of Khonsu
Nebet Het(Nephthys): sister of Aset and unwilling wife of Set
Neith: creator goddess and defender of the sun god
Nekhebet: protective vulture Goddess of southern Kemet
Neper: God of grain
Nerit(Neret): Goddess of strength
Nu: the primal water
Nun: God of the primeval ocean
Nut: sky Goddess and mother of Asar, Aset, Nebet Het, Set, and Heru Ur
Pakhet: a cat Goddess
Papait(Papaet): Goddess of birth
Pestit: Goddess of sunrise
Pestu: God of light
Ptah: creator God of Memphis and patron of artists and craftsmen
Ra: creator sun God and Ruler of the Universe
Rekhet: Goddess of knowledge personified
Remi: a fish God
Remnet: a cow Goddess
Renenutet: Goddess of the harvest, depicted as a cobra, said to be present at childbirth and is the one who decides how long the child will live
Renpiti: a God of time
Saa: the God of touch
Sekhmet: ferocious solar lion Goddess
Seshat "She who writes" known as the Lady of Literature and Libraries, Goddess of Architecture and Record Keeping, supposedly the wife of Djehuty but I think I read somewhere that they said She was also possibly His daughter
Set(h): desert and storm God, enemy of Asar, rival of Heru, and strongest of the Gods
Setem: the God of hearing
Shai: a God of destiny, each of us have our own Shai
Shesmu: a God of wine
Shu: God of air and sunlight who separated the earth and sky
Sia: this God personifies the perseceptive mind
Sobek(Sebek): primeval crocodile God and Lord of the Nile
Sokar: Memphite God of death and regeneration
Tait: a Goddess of weaving
Tanent: primal earth Goddess
Tauret: protector of women in childbirth, symbolized by the hippopotamus
Tefnut: sister of Shu and mother of Geb and Nut
Tem (Atum, Temu): creator deity of Heliopolis and evening form of the sun God
Un: God of existence
Unit(Uneet): a star Goddess
Unta: a God of light
Unti: a God of light
Ur Henu: a water God
Utchait: a Goddess of the moon
Utekh: a God of embalming
Utet Tefef: god of the 29th day of the month
Wadjyt(Uadjet): protective cobra Goddess of the north
Wenut: An Arrow of Bast and Eye of Ra

Sources: Circle of Isis: Ancient Egyptian Magic for Modern Witches
Kemet.org
Ancient Egypt Online
And others.