S##E## means Season ## Episode ##. S##SP## means Season ## Special ##.

Doctor Who #1 (2008) - Takes place between S03E06 and S03E11.
Doctor Who #2
Doctor Who #3
Doctor Who #4
Doctor Who #5
Doctor Who #6

Doctor Who: The Whispering Gallery #1 (2009)

Doctor Who: Black Death White Life #1 (2009)

Doctor Who: Autopia #1 (2009) - Takes place between S04E01 and S04E11.

Doctor Who: Cold-Blooded War #1 (2009)

Doctor Who: The Forgotten #1 (2008) - Takes place between S04E13 and S04SP01.
Doctor Who: The Forgotten #2
Doctor Who: The Forgotten #3
Doctor Who: The Forgotten #4
Doctor Who: The Forgotten #5
Doctor Who: The Forgotten #6

Doctor Who: The Time Machination #1 (2009) - Probably takes place between S04SP00 and S04E01.

Doctor Who: Room with a Déjà View #1 (2009)

Doctor Who Vol. 2 #1 (2009) - Takes place between S04SP02 and S04SP03.
Doctor Who Vol. 2 #2
Doctor Who Vol. 2 #3
Doctor Who Vol. 2 #4
Doctor Who Vol. 2 #5
Doctor Who Vol. 2 #6
Doctor Who Vol. 2 #7
Doctor Who Vol. 2 #8
Doctor Who Vol. 2 #9
Doctor Who Vol. 2 #10
Doctor Who Vol. 2 #11
Doctor Who Vol. 2 #12

Doctor Who Annual 2010 #1 (2010)

Doctor Who Vol. 2 #13
Doctor Who Vol. 2 #14
Doctor Who Vol. 2 #15
Doctor Who Vol. 2 #16

Doctor Who: A Fairytale Life #1 (2011) - Takes place between S05E01 and S05E06.
Doctor Who: A Fairytale Life #2
Doctor Who: A Fairytale Life #3
Doctor Who: A Fairytale Life #4

Doctor Who Vol. 3 #1 (2011) - Takes place between S05E13 and S06E01.
Doctor Who Vol. 3 #2
Doctor Who Vol. 3 #3
Doctor Who Vol. 3 #4
Doctor Who Vol. 3 #5
Doctor Who Vol. 3 #6
Doctor Who Vol. 3 #7
Doctor Who Vol. 3 #8

Doctor Who Annual 2011 #1 (2011)

Doctor Who Vol. 3 #9
Doctor Who Vol. 3 #10
Doctor Who Vol. 3 #11

Doctor Who: 2011 Convention Special #1 (2011)

Doctor Who Vol. 3 #12
Doctor Who Vol. 3 #13
Doctor Who Vol. 3 #14
Doctor Who Vol. 3 #15
Doctor Who Vol. 3 #16

Star Trek: The Next Generation/Doctor Who - Assimilation² #1 (2012) - Takes place between S06SP01 and S07E05.
Star Trek: The Next Generation/Doctor Who - Assimilation² #2
Star Trek: The Next Generation/Doctor Who - Assimilation² #3
Star Trek: The Next Generation/Doctor Who - Assimilation² #4
Star Trek: The Next Generation/Doctor Who - Assimilation² #5
Star Trek: The Next Generation/Doctor Who - Assimilation² #6
Star Trek: The Next Generation/Doctor Who - Assimilation² #7
Star Trek: The Next Generation/Doctor Who - Assimilation² #8

Doctor Who Special 2012 #1 (2012) - Takes place between S07E03 and S07E05.

Doctor Who Vol. 4 #1 (2012)
Doctor Who Vol. 4 #2
Doctor Who Vol. 4 #3
Doctor Who Vol. 4 #4
Doctor Who Vol. 4 #5
Doctor Who Vol. 4 #6
Doctor Who Vol. 4 #7 - Takes place between S07SP01 and S07E06.
Doctor Who Vol. 4 #8
Doctor Who Vol. 4 #9 - Takes place between S07E09 and S07E13.
Doctor Who Vol. 4 #10
Doctor Who Vol. 4 #11
Doctor Who Vol. 4 #12
Doctor Who Vol. 4 #13 - Takes place between S07E12 and S07E13.
Doctor Who Vol. 4 #14
Doctor Who Vol. 4 #15
Doctor Who Vol. 4 #16

Doctor Who Special 2013 #1 (2013) - Takes place between S07SP02 and S07SP03.

Doctor Who 50th Anniversary Blu-ray Special #1 (2013)

Doctor Who: Prisoners of Time #1 (2013)
Doctor Who: Prisoners of Time #2
Doctor Who: Prisoners of Time #3
Doctor Who: Prisoners of Time #4
Doctor Who: Prisoners of Time #5
Doctor Who: Prisoners of Time #6
Doctor Who: Prisoners of Time #7
Doctor Who: Prisoners of Time #8
Doctor Who: Prisoners of Time #9
Doctor Who: Prisoners of Time #10
Doctor Who: Prisoners of Time #11
Doctor Who: Prisoners of Time #12