Roots: Slow Decay. Martha's alias Samantha Jones is a reference to the eighth Doctor's companion in the BBC novels.
Goofs: Meredith Roberts' date of birth is given as 11/01/1962 on his driving licence, so why does Owen say he was 45 years old, when it's very well established that this season of Torchwood takes place in 2008? [Owen didn't see the license, and misheard the date of birth when someone else said it.]
The way the reset drug is explained it apparently gets rid of anything in the body that isn't part of the human. In reality this would cause immense damage, as the human body relies on bacteria that don't share human DNA in order to function - particularly in the digestive system.
How does Professor Copley deduce that Martha has travelled in time and space simply from differences in her white blood cells?
Martha has only been injected with the reset drug for a couple of hours at most when Professor Copley says she's the only subject where the mayfly has survived to the larval stage. Even if she was given a particularly concentrated dose, other subjects have clearly had mayflies incubating in their bodies for weeks. It simply isn't plausible for them to have developed that quickly in Martha.
Continuity: Martha is now a qualified doctor. She was recruited by UNIT after a recommendation that's implied to be the Doctor. Her immune system has been changed by her travels in the TARDIS. She is engagesd to a man who actually did save her life (implied, but not actually stated, to be the guy she met in Last of the Time Lords).
Torchwood tech includes contact lenses that act as cameras when worn and allow the wearer to receive text messages.
The Pharm is a medical research institute that tries to get cures from captive aliens. It is government backed, though its source of alien bodies is never revealed. [Since it isn't known to UNIT or Torchwood, maybe it was connected to the Forge from the Big Finish audios.]
Links: There's a newspaper showing Margaret Blaine as mayor of Cardiff (Boom Town). There are numerous references to Martha's adventures with Jack (Utopia, The Sound of Drums, Last of the Time Lords).
Extras: This episode of Torchwood has an episode of Torchwood: Declassified
Location: Cardiff, 2008.
The Bottom Line: 'I'm here to complete your post-mortem.' Freema Agyeman walks on set and then completely steals the show in an absolutely brilliant performance. The writing's not bad either.