Footage of the extermination of security guard Bywater in Dalek (2005) and the Dalek attack on the Valiant in The Stolen Earth (2008) is seen in 'Rusty's' Dalek memories, and the destruction of the Daleks and the Crucible in Journey's End (2008) is seen when Rusty looks into the Doctor's mind.
According to Lance Parkin's Whoniverse: An Unofficial Planet-By-Planet Guide to the Universe of the Doctor, from Gallifrey to Skaro, the script specifies that the story takes place in the 31st century.
The Doctor tells Clara that is not possible for the Dalek to be good because there's "no such thing as a good Dalek." The first version of Clara seen on the show, in Asylum of the Daleks (2012), was a Dalek, who sacrificed herself to help The Doctor, Amy, and Rory.
The Vent joke exchanged between The Doctor and Clara is a reference to the vent scenes from The Ark in Space: Part Four (1975) between the Fourth Doctor and Sarah Jane Smith. It also reflects a similar exchange between Rose Tyler and Toby Zed in The Satan Pit (2006).
Rusty says "Resistance is futile", a catch phrase famously associated with the Borg race from the American science fiction series "Star Trek", but which was first used on Doctor Who by the Cybermen in 1967.