The phrase "The Once And Future King" is taken from the title of T.H. White's four book series of Arthurian tales, the first of which was used as the basis for Disney's The Sword in the Stone (1963). White derived his title from the inscription that, according to Thomas Malory's Le Morte d'Arthur, was written upon King Arthur's tomb: "Here lies Arthur, king once, and king to be." It was White who first described Merlin as living through time backwards; an idea revisited by Joe Cornish in this movie.
The address on the flyer for the restaurant where Merlin insists Alex meet him is 8 Boorman Road (at 0:24:29-0:24:33). John Boorman co-wrote, produced and directed Excalibur (1981).
The Stonehenge Tour Guide is played by Adam Buxton who has been the comedy partner of writer/director Joe Cornish since the 1990s when they created and hosted The Adam and Joe Show (1996) together.
When introducing himself to the class, young Merlin gives his name as "Mertin Ambrosius Caledonensis". The first name is, of course, a sly play on "Merlin" he made up on the spot, but other two names are derived from names used to refer to the wizard Merlin in the legend of King Arthur and stories that inspired the character. Merlinus Caledonensis is another name for the Welsh folk character Myrddin Wyllt (the name means "of town of Carmarthen", a place in South Wales,) while Merlin Ambrosius is the given name of the Merlin character in the original Arthurian story Historia Regum Britanniae by Geoffrey of Monmouth.
Patrick Stewart also played Leondegrance (Guinevere's father) in Excalibur (1981), one of the prime inspirations for this movie.