Deep Space 9. Destroyed in 2383 in Typhon Pact - Plagues of Night. Still active in 2410 in STO.
The Terran Rebellion. In the novels, they establish the peaceful Galactic Commonwealth. In STO, they restore the Terran Empire.
The mushroom-looking species from ENT - "Silent Enemy". In ENT - Rise of the Federation: A Choice of Futures, they have little understanding of humanoid lifeforms and did not understand that they were being threatening. They are also the offhandedly mentioned mute species of Gamma Vertis IV from TOS - "The Empath". In STO, they are called the Elachi and are servants of the Iconians.
The solanogen-based species from TNG - "Night Terrors". In TTN - Sight Unseen, they are revealed to be the sole intelligent species which is trying to escape a collapsing pocket dimension. In STO, they are a scientist caste of the Iconians who were accidentally exiled into subspace.
The neural parasites from TNG - "Conspiracy". The DS9 novels portray them as mutated Trill symbionts hailing from the extinct colony mentioned in TNG - "The Chase". Said parasites seek revenge on the Trill. In STO, the parasites are servants of the Iconians.
The Iconians. In the novels, they are a colossal species and exodused the Milky Way to go exploring places where their gateways could not reach. In STO, they are a human-sized semi-incorporeal species, and they return and try to conquer the galaxy.
Kal Dano, the unseen inventor of the Tox Uthat from TNG - "Captain's Holiday". In DTI - Watching the Clock, the Vorgons explain that he invented the Tox Uthat to destroy the Vorgon sun and civilization in the past. Subsequently, Daniels's colleague Jena Noi arrests Ajur and Boratus. In STO, he is a mixed-species non-villainous Federation scientist. Agent Daniels gives him a time travel pod, and he goes to save one of his ancestor species in the 25th century. After the Tholians steal the Tox Uthat, he and the player character retrieve it and hide it on 22nd century Risa. Dano is later killed and becomes the corpse from ENT - "Future Tense". The player character and a 29th century temporal agent retrieve his corpse. And it turns out that Picard tricked the Vorgons in "Captain's Holiday" and the Tox Uthat survived. The player and Daniels chase the Vorgons to the Uthat's storage place in 2375, during the Breen attack on Earth. In a confrontation, the player kills Ajur, prompting Boratus to join forces with the Future Guy from ENT. In a later mission, the player installs the Uthat aboard the Enterprise-J at Procyon V in the 26th century to destroy the Sphere Builder's sphere network.
Also, it turns out that Future Guy sent his Na'kuhl allies to 2268 so that when a Na'kuhl ship and a Tholian ship were mutually destroyed, the interphasic rift it generated would swallow up the U.S.S. Defiant (NCC-1764) to be found by mirror universe Archer. Aboard the Defiant was a message which Admiral Leeta would eventually see, prompting the Terran Empire to join Future Guy's Temporal Liberation Front.
The reason why the Tholians targeted the time travel pod in ENT - "Future Tense". DTI - Watching the Clock indicates that it was temporal policing action. STO implies that Tholians have a greater awareness of spacetime and were seeking the pod for their own technological advancement.
The shadowed sponsor of the Suliban Cabal from ENT. DTI - Watching the Clock portrays him as a 28th century mixed species genetic engineering supremacist. STO portrays him as a 25th century Krenim scientist.
The Breen. They are a multispecies confederation in the novels. In STO, no such indication is made.
Species 8472. In the novelverse, they prefer to be called Groundskeepers. Their home dimension, fluidic space, is a multiversal singularity. An alternate reality Voyager crew gives them a device which seals off access to their home from the outside. In STO, the multiversal singularity aspect is absent and they are called Undine. The Iconians access fluidic space with ease and manipulate them into attacking Alpha Quadrant powers.
The planet Galorndon Core from TNG - "The Enemy" and Chulak, the Romulan commander mentioned in VOY - "The Thaw". ENT - The Romulan War: To Brave the Storm portrays him as a 22nd century Romulan commander who rammed his ship into Galorndorn Core, turning it into a hellhole planet. Star Trek Online portrays Chulak as a 23rd century Romulan commander who allies with time-traveling Na'kuhl. When the alliance's doomsday machine goes out of control, it crashes into Galorndorn Core, also turning it into a hellhole.
They're not mutually exclusive, though--IIRC Watching the Clock suggests that the uptime factions have been/are/will be preventing the Borg from assimilating time travel tech, so maybe the only way they could acquire the technology was from the Sphere Builders.
