When Queen Elizabeth kisses the Tenth Doctor, the War Doctor asks, "Is there a lot of this in the future?" and the Eleventh Doctor responds "It does start to happen, yeah.", referencing the fact that The Doctor was not allowed any romantic attachments (and no kissing scenes) during the classic era of Doctor Who (1963).
The War Doctor's regeneration was only shown half-completed because Christopher Eccleston declined to return and Steven Moffat wanted to respect his decision, on the grounds that making it appear that an actor was in something they did not want to be in without their consent would be unethical.
During his incarceration, the Eleventh Doctor carves the base code of the vortex manipulator into the wall of the tower of London for Clara. The base code is the exact time Doctor Who (1963) was originally broadcast: 1716231163 or 17:16 23/11/63.
John Hurt did not actually audition for The War Doctor, but had been asked by the production team and "said yes with remarkable speed".
Christopher Eccleston took several meetings with Steven Moffat regarding reprising his role as the Ninth Doctor, but ultimately had to drop out due to scheduling issues and there not being a script ready. He also wanted Joe Ahearne to direct, as he felt that he was the best director of his season, but an agreement could not be reached.