Brown was a colour.
Numerous incarnation of the Doctor had brown coloured hair. The Tenth Doctor had thick brown hair and deep, brown eyes. (TV: The Parting of the Ways, Children in Need Special) One of the two main suits he wore during this incarnation was dark brown with blue pinstripes. (TV: The Christmas Invasion) Other incarnations with brown hair include the Fourth, (TV: Planet of the Spiders) Seventh, (TV: Time and the Rani) Eighth, (TV: Doctor Who) War (TV: The Night of the Doctor) (after regenerating), Ninth (TV: Rose) and Eleventh Doctors. (TV: The End of Time)
Many of their companions possessed brown hair, some being Peri, (TV: Planet of Fire) Clara, (TV: The Bells of Saint John) Sarah Jane, (TV: The Time Warrior) Rory (TV: The Eleventh Hour) and Jack. (TV: The Empty Child)
Individuals or species the Doctor met with brown eyes included the Tactires, (COMIC: The Forgotten), Marnal, (PROSE: The Gallifrey Chronicles) Jane McKillen and Dale Hicks. (TV: Fear Her)
In Through the Eye of Eternity, the Brown Eye of Eternity only appeared once, in the 1996 episode "Miss Hiroshima". (PROSE: The Book of the War)