Merlin the Wise

A manipulative and sinister figure calling himself Merlin the Wise, (COMIC: The Neutron Knights) native to Earth, (COMIC: The Tides of Time) sought the Doctor's help on two occasions.

The Fourth Doctor first met Merlin in the distant future of Earth. Merlin had appeared from another time period to help the Neutron Knights against their enemy Catavolcus. Merlin had summoned the Doctor himself to help. (COMIC: The Neutron Knights)

They next met in the Matrix on Gallifrey where Merlin had joined a council of High Evolutionaries, including Rassilon, founder of the Time Lords, to discuss the danger posed to the universe by the "demon" Melanicus. The Fifth Doctor did not entirely trust Merlin but agreed to his aid. Merlin had originally banished Melanicus from the universe, though, obviously he had not managed to make it permanent. (COMIC: The Tides of Time)

He was later replaced among the Evolutionaries by a member of the Order of the Black Sun. (COMIC: The Final Chapter)

Behind the scenes
The Creation of Camelot showed that in the Doctor Who universe, the title of Merlin was passed on from one individual to the next, being more of an office in King Arthur's court than a name. Individuals known to have held the title of Merlin included an otherwise-unknown human being who died "on the job" and an incarnation of the Master (both in The Creation of Camelot), the Eighth Doctor as well another otherwise-unnamed renegade Time Lord (both in One Fateful Knight, with the Eighth Doctor also reusing the alias in The Shadows of Avalon), and most strikingly, a mysterious future incarnation of the Doctor mentioned throughout Battlefield, potentially the last-ever incarnation of the Doctor.

Thus, it is unclear if the "Merlin the Wise" seen in The Neutron Knights and  The Tides of Time was one of these various established Merlins, or another claimant to the name altogether — although he, of course, does not resemble the Eighth Doctor or the "Merlin" Master, crossing off two suspects.

Whoever he may be, this Merlin has a link to the Marvel UK universe (and, more remotely, to the Marvel Universe generally). He appears in a cameo in the Marvel UK comic book Captain Britain as the Marvel Universe Merlin (in another form) shows off some of the other forms and personalities he has, at times, assumed. In the later Captain Britain and MI13, writer Paul Cornell explicitly had them as the same Merlin and also made reference to the High Evolutionaries.
 * A different Merlin is an unseen figure in the Seventh Doctor television story Battlefield as a future incarnation of the Doctor. Many accounts say this was a red-haired incarnation of the Doctor. (PROSE: Battlefield, Happy Endings, et al)
 * According to One Fateful Knight by Peter David, Merlin was another renegade Time Lord altogether.