Underworld

Naruto - Persephone (Goddess of Spring, Flowers, and Vegetation: Born of Demeter and Zeus, However depending upon the myth she was known by many other titles)

Madara - Hades (God/Ruler of the Underworld, The Dead, and Riches: Born of Cronus and Rhea)

Itachi - Melinoe (Goddess of Nightmares and Madness: Born of Persophone and Hades)

Sasuke - Macaria (Goddess of Blessed Death: Born of Hades, Mother Unknown)

Indra - Thanatos (God of Death/The personification of Death: Born of Nyx and Erebus)

Hinata, Neji, and Hanabi - Erinyes (Deities of Vengence) 

Shisui - Oneiroi (God/Deity of Dreams: Born of Nyx and Erebus)

Olympus

Hashirama - Zeus (God/Ruler of Mortals, Law, Order, Justice, and Thunder: Born of Cronus and Rhea)

Minato - Demeter (Goddess of Agriculture, Harvest, Fertility, and Sacred Law: Born of Cronus and Rhea)

Tobirama - Poseidon (God of the Sea, Storms, and Earthquakes: Born of Cronus and Rhea)

Shikamaru - Athena (Goddess of Battle, and Battle Strategy: Born of Metis and Zeus)

Izuna - Ares (God of War) 

Titans

Tajima - Cronus A/N: Hence the 'Son of Uchiha part'

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Tell me if I missed anyone I mentioned because I'm not sure I got everyone.