Aven

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Aven is Bert's daughter and the captain of the Dragonship the Indigo Dragon. Young, attractive, tough, smart, and brave, Aven quickly attracts the attentions of Jack and Artus (then Bug), but she seems unwilling to admit whether or not she reciprocates either young mans' feelings. Indeed, it is revealed in The Search for the Red Dragon that, while she agreed to marry Artus to help rule the Archipelago, but the engagement ended when Aven realised she was not happy away from the sea, but she continued to hold the title of queen. It is also revealed she was in love with Captain Nemo and that he, not Artus, is the father of her son, Stephen. Aven does not appear in The Indigo King (oddly, as it references her old Dragonship), but reappears for The Shadow Dragons.

Rose Dyson

Rose is the daughter of Mordred and the so-called "Holy Grail," which turns out to have been a beautiful young woman being held in the Library of Alexandria, and who becomes one of the Fates. Rose is taken from her mother by the Caretakers in The Indigo King so that she can resurrect King Arthur. Rose is taken back to the Summer Country, where she lives with Hugo Dyson (hence her surname) but where she does not age, and where she is not visible to everyone. Rose becomes crucial in The Shadow Dragons, when she must confront her father (as Mordred) and wield Excalibur, the only weapon that could hope to defeat the Winter King. 

Laura Glue

Laura Glue is the granddaughter of Peter Pan. She first appears in The Search for the Red Dragon when she appears in Jack's garden while trying to find JM Barrie. Insistent upon being called by her whole name (which she created by herself), she is one of Peter's "Lost Boys," and she is thereby crucial to the Caretaker's adventures in the second novel. She ages some over the novels and, by The Shadow Dragons, is the leader of the Valkyries; it is also hinted she has a romance with Stephen.

Artus/Bug

Artus is the King of the Archipelago of Dreams. Once called "Bug" (when he was the pot-boy to the Fates on Avalon), it is discovered to be a descendant of King Arthur, and therefore the heir to the throne of the Archipelago. Eager to join the Caretakers on their adventure in Here, There Be Dragons, Artus dreams of being a knight, having been inspired by the so-called Green Knight, who guards Avalon. He - like Jack - quickly becomes attracted to Aven, and, as the novel comes to a close, becomes engaged to her. It is revealed, however, in The Search for the Red Dragon that the engagement falls through when Aven realises she cannot stand being away from the sea, but she still retains the title of "queen." (It is also revealed that Aven's son, Stephen, is not biologically Artus' son (rather, Captain Nemo's), but that he raises him as his own anyway.) Despite being "king," Artus makes the Archipelago a democracy in the hopes of making it more just. He is killed in The Shadow Dragons, but it is unknown if he will "stay dead."
Stephen, Aven's son with Captain Nemo (conceived most likely sometime during the first novel) he is taken under the King of Cricket's spell in the second novel, but rescued by Aven, his surrogate father Artus, and the Caretakers. He is shown to be as strong a fighter as both his parents, and it is hinted he may have a romance with Laura Glue.
Captain Nemo, the captain of one of the seven Dragonships. He is shown to have had a close friendship with Aven, but it is not revealed until the second novel that they were lovers and share son, Stephen. Nemo is fearless, dedicated, and self-sacrificing. In the battle at Terminus, Jack accidentally causes Nemo to lose his life, which shakes Jack terribly. However, in The Shadow Dragons, Nemo "returns," albeit in a reincarnated, younger form.
The Winter King/Mordred, the series' main villain and the twin of Merlin. Known as Mordred, the Winter King, or the King of Crickets, every novel includes his new attempts to take over the Archipelago and, by extension, the Summer Country. As "Mordred," he fathered, with the Holy Grail, a daughter, Rose; also as Mordred, he tried to become King of Briton, but was thwarted by a boy, Thorn (who would later become Arthur). In The Shadow Dragons, Rose visits her father, who is at the bottom of the waterfall at the Edge of the World (while his Winter King alter-ego is wrecking havoc in the Archipelago) and who is the only person who can re-weld Excalibur; however, in payment, Rose brings Mordred a door to escape the Edge of the World. 

The Cartographer/Merlin, the former magician punished to draw maps until a descendant of Arthur released him. Originally called Merlin, he puts aside that identity to embrace his isolation as the Cartographer in the Keep of Time. He is the twin brother of Mordred, and thereby the uncle of Rose, the descendant of Arthur who releases him from his duties. Though he assists the Caretakers throughout their adventures, he is hardly ever terribly concerned with the events that take place outside his Keep. 
Don Quixote, the "fictional" Spanish knight who assists the Caretakers in The Shadow Dragons. He becomes a guardian of sorts to Rose, and accompanies her and Archimedes everywhere.
Richard Burton
Archimedes
Tummeler
Uncas
Fred
Peter Pan
Lancelot
Arthur
The Lady of the Lake
Harry Houdini
Arthur Conan Doyle
Hugo Dyson
The Fates
Chaz
Magwich
Geoffrey of Monmouth
The Holy Grail
Daedalus
Ordo Maas
Samanranth