When Captain Jack mocks the Doctor and Rose for their out-of-place outfits ("Flag Girl was bad enough - but U-boat captain?"), he is actually spot on - the Doctor's leather jacket is in fact a vintage 1938 German U-boat commander's jacket.
The hospital where The Doctor meets Dr. Constantine, Albion Hospital, is the same hospital where they took the "Space Pig" in Aliens of London (2005).
Dr. Constantine remarks that he used to be both a father and grandfather, but is now neither. The Doctor replies that he "knows the feeling," implying that his granddaughter; a lead character in the first few seasons of Doctor Who (1963); has since died, probably during the Time War.
The nanogenes were originally called nanites; the new terminology was suggested by script editor Helen Raynor after it was observed that nanites were a plot device often used in Star Trek.
Jack is a former Time Agent. They were first mentioned in The Talons of Weng-Chiang.