Merlin

Merlin was a Time Lord posing as a magician in an alternate universe.

Profile
The Doctor first learnt of Merlin while fighting Merlin's enemy, the sorceress Morgaine in 1990s Cornwall. Ancelyn from Arthur's world identified the Doctor as Merlin, even though he did not recognize his face. The Doctor thought that Ancelyn may have known an alternative and/or future incarnation of the Doctor himself. According to Ancelyn, Merlin had a ship like the TARDIS and would get imprisoned by Morgaine. He also left a note for the Doctor which he recognized as in his own handwriting. (DW: Battlefield) The Doctor would later meet, Muldwych a future incarnation of himself who may have posed as Merlin. (NA: Happy Endings)

Whilst stuck in the otherworld of Avalon, the Doctor attempted to pass himself off as Merlin to Queen Mab. (EDA: The Shadows of Avalon)

The condundrum of Merlin's true identity was apparently resolved when the Doctor travelled to Arthur's reality to aid in his birth; as the Doctor discovered, he was only the second Merlin, the other one being another renegade Time Lord who had given Arthur and his kingdom advanced technology, prompting Morgaine to seek an alliance with them. This other Merlin, disguised as the Doctor, was imprisoned in the Arctic by Morgaine after she was temporarily banished to a desert by the Doctor, leaving the Doctor to set up the events that would later be experienced by his seventh incarnation. (ST: One Fateful Knight)

Other information
The Doctor had earlier met a High Evolutionary known as Merlin the Wise. (DWM: The Neutron Knights, The Tides of Time)

Behind the scenes
In 2008, Julie Gardner became producer of the BBC Wales production, Merlin, a reimagining of the Merlin and King Arthur legend, and which featured numerous Doctor Who and Torchwood cast and crew members. Although there was some initial fan speculation as to whether it would be possible to reconcile the new series with the version of Merlin presented in Doctor Who, the new concept of the character doesn't allow for this.