Cyborg Helmsman

In nearly every Ship Based Science fiction novel of relative hardness your search for the most heavily augmented individual will usually end at one of two people, the grizzled war veteran, or this guy, the ship's navigator. Why? Maybe they need more brainspace for all the calculations necessary to adjust the ship's position in Warp Space, or they need better reaction times, or maybe they really need those Electronic Eyes to find and follow the normally invisible "Safe Zones" in hyperspace.

Can have different gradations, as the concept starts at replacing controls that require muscle action with Brain-Computer Interface to reduce delays and increase resistance to acceleration and vibration, goes through general and purpose-built augmentation, and ends at Brain In a Jar wired into controls.

Examples of Cyborg Helmsman include:

Crimson Dark
The Navigators of Dune arguably qualify, albeit without the usual biomechanical augmentation; they use Spice.
Flight of the Navigator plays with this a little, where the robotic ship needed to store some of it's data in a human brain while it rebooted itself. After redownloading that data a little Humanity Is Infectious takes place and the ship develops some very human emotions and personality.
Sandstrom the "augumented human" in Hyperdrive is a buggy prototype. It's not clear that her Unusual User Interface is actually any better than a normal helmsman would be.
Outlaw Star has Melfina, an artificial human, as a helmsman.
Katherine Kerr's Polar City Blues has Lacey, a former (space) Navy pilot who has a neural-link port implanted in the back of her neck for connecting to ships, which has since sealed over.
Vatta's War uses implants that allow access to certain funtionalities not normally allowed, as well as allowing mental activation and use of some controls.
In the Vorkosigan Saga, starship pilots need special implants to interface with ship's navigation during wormhole travel. A recurring character is Arde Mayhew, who is unable to receive upgraded implants for medical reasons and so can't pilot more recent models of ship, and in The Warrior's Apprentice faces disaster with the decommissioning of the last remaining ship he is able to pilot.
The protagonist of Sergey Lukyanenko's Genome is a genetically and, to a lesser degree, cybernetically augmented starship navigator. In a subversion, though, almost every human in the story is similarly enhanced (except the "natural" engineer).
In spite of Star Trek's usual stance on cybernetics and transhumanism, Geordi LaForge wore a VISOR that connected to his brain and allowed him to see. In the first few seasons, his role on the ship was as the Helmsman, although he eventually graduated to Chief Engineer.
The Navigators of Warhammer 40,000 are mutant helmsmen, capable of navigating through the Warp and allowing the Imperium to exist.
- Also, some ship captains, especially on Adeptus Mechanicus ships. One such captain appears in the first Gaunt's Ghosts book.
- 40k uses the entire spectrum from unobtrusive Brain-Computer Interface to lifesupport sarcophagi wired into vehicle bodies, and from consumer grade vehicles to capital spaceships.
In the Revelation Space universe, the crews of interstellar spacecraft have formed their own culture, and most of them are cyborgs. A more extreme example is John Brannigan, a starship captain who became infected with a nanotechnological virus, causing his mind and body to merge with his ship in a very disturbing way.
In Homestuck, this is the ultimate fate of the Psiioniic, with a dose of Body Horror thrown in for good measure - with his incredible psychic abilities, he's implied to not only steer but also power the Condesce's flagship, to which he is literally fused.
Ship captains and pilots in Peter F. Hamilton's Nights Dawn Trilogy have extensive neural implants for controlling the ship and mapping out trajectories. Physically modified Cyborgs are primarily used as engineers and for patching up damage - some of them are so heavily modified that they don't even need space suits to survive in the vacuum, instead just needing a bottle of oxygen.
Star Frontiers has "Cybernetic Robots" with organic parts, i.e. Brain In a Jar combined with robotic brain and body. There are "cyber freighters" run by a cybot captain with the crew of common robots - but they are rare. One Knight Hawks adventure deals with a freighter that gone missing only to reappear later on collision course with a space station, after its cybot captain gone mad. If this sort of things happened repeatedly, this may explain lack of popularity.