Although this might be considered a list based questions the full answer's validity will not change with time as there was a finite list of Greek and Roman deities and that will not change in the future. Which Greek deities do not have an "equivalent" in the Roman pantheon and vice versa?
The gods that I know-
- Bellona - Roman goddess of war
- Lupa- Roman wolf goddess
- Janus- 2 headed Roman god
- Pomona- god of plentiful
- Achelois - One of the Greek moon goddesses.
- Achelous - The Greek patron god of the Achelous river.
- Alastor - Greek god of family feuds. (ikr)
- Alcyone - One of the seven daughters of Atlas and Pleione. (greek. is she a goddess?)
- Alectrona - Early Greek goddess of the sun.
- Antheia - Goddess of gardens, flowers, swamps, and marshes.
- Astraea - The Star Maiden - a goddess of justice, included in Virgo and Libra mythologies.
- Até - Goddess of mischief.
- Bia - The goddess of force.
- Brizo - Protector of Mariners.
- Celaeno - The name of a wife of Poseidon.
- Dinlas - Guardian of the ancient city of Lamark, where wounded heroes could heal after battle.
- Doris - A Sea Nymph, mother of the Nereids. (guess this counts as a goddess)
- Eireisone - The deity who embodied the sacred ceremonial olive branch.
- Iris - Goddess of rainbows.
- Khione - The goddess of snow and daughter of the North Wind (Boreas).
- Kratos - A god of strength and power.
- Merope - One of the seven Pleiades, married to king Sisyphos. (goddess or not?)
- Morpheus - God of dreams and sleep.
- Plutus - God of wealth.
- Pricus - The immortal father of sea-goats, made into the Capricorn constellation.
- Styx - A Naiad who was the first to aid Zeus in the Titan war. (Not to be confused with the river Styx).
- Zelus - The god of zeal, rivalry, and jealousy.
- Atlas - The Primordial Titan who carried the world on his back.
- Metis - Titan goddess of wisdom.
- Oceanus - Titan god of the ocean.
- Pallas - A giant who was one of the ancient Titan gods of war. (?)
If you think the muses are gods then those too.
Orcus is a Roman-specific deity. He's the god of Demonic Torment of damned souls. If he was Greek, he'd have worked in the Fields of Punishment.
Thanatos is one I know of. The Romans felt that trying to rename death wouldn't be very wise.