In doing this, I was aiming to make a timetable that is as canonical as possible while still being consistent. However, as we all know, canon is not 100% consistent, so there are some points on which this timeline will appear to contradict canon-- most notably, I place DW 1.01 Rose in 2004, even though the poster in Aliens of London says she disappeared in 2005. If we accept that this was an error, most of the other timeline stuff works out pretty well, but if we say that Aliens of London was, in fact, in 2006, we end up with a whole new batch of inconsistencies.
Please note that this timeline contains spoilers for everything that has been aired up to this point. As always, please feel free to make suggestions/tell me if I've gotten something heinously wrong.
1. There are several plausible explanations for Jack being away for what seems like at least a couple of months in between End of Days and Kiss Kiss, Bang Bang, even though the whole DW S4 arc only seems to cover a few days in the "present" time-- I've gone with the explanation offered by lorannah because I like it best, and because it means that everything fits in well in terms of the time passed between the fall of Harriet Jones and the election of Harry Saxon-- this explanation suggests that the Doctor went back in time a few months to take advantage of the Rift energy caused by the TW team in End of Days-- after the events of Utopia, however, the Doctor takes Martha back to her proper timeline-- which means that Jack skipped a few months. However, it is still possible to make it work if you set the "present" of DW S3 in February 2007, and simply say that the TARDIS accidentally set Jack back in Cardiff a few months too late.
2. With regard to timeline info revealed in TW 2.12 Fragments, assumed that when something is referred to as X years ago, they are simply subtracting the year it happened from 2008-- hence, Owen's story, which begins in 2004, is "Four years ago" even though, even though according to my timeline, it's more accurately 3.5 years. When they want to be more specific, they give the time period in months, as with Ianto's story. This also works with Jack's need to be frozen for 107 years in 1901.
3. I have also, as far as possible, tried to match the timeline to the season it is shown to be in the show. It is not always possible to get an exact match (for instance, the kids in SJA seem to be running around in light clothing even in November), but I've tried to deal with the really glaring ones-- for instance, it is obviously well into Autumn in The Sontaran Stratagem/The Poison Sky, so I put it in October. In Adrift, Gwen and Rhys eat outside under leafy trees-- while it pretty clearly looks summery, I put it in April-- I figured it might have just been a particularly warm day, possibly later in the month.
4. I've decided to ignore the timeline of the Turn Left!verse-- it simply doesn't fit in with the "real" timeline, so we have to assume that, even though a lot of the same events occured, they occured at slightly different times, due to the AU-ness (for instance, Turn Left suggests that Luke, Maria, Clyde and Sarah Jane all died in Smith and Jones-- but none of them had met each other yet at that point in the real!verse).
5. Lastly, I'm sure that the new Season of SJA coming up at the end of the month will shit all over this timeline. :P According to me, this season of SJA should start somewhere between November and January 2009 (that is, roughly a full year after the conclusion of S1), but I bet you anything that they decide to set it just before the start of the school year again-- which will suggest that the DW finale took place during the summer (and that doesn't work in so many ways-- it conflicts with Lost Souls being both in September and before the DW finale, it'll mean that the streets were full of red and yellow foliage in the middle of June, for frak's sake-- argh!). Until then though, this is what works. :)
January 2000: (Jan 1) Jack Harkness takes over Torchwood Three as leader.
January 2000 thru December 2002: Jack cuts all ties with Torchwood One; Recruits Suzie Costello (I'm assuming that Suzie was recruited before Tosh and Owen because she was 2IC in Everything Changes).
March-June 2003: Toshiko Sato creates sonic modulator; is imprisoned by UNIT (roughly five years before Fragments in 2008).
July-October 2003: Jack recruits Tosh and has her record wiped (roughly three years before Greeks Bearing Gifts in 2006).
March 2004: DW 1.01, Rose
November 2004: Owen Harper's fiance, Katie, dies due to alien in her brain. Owen meets Jack for the first time, and is given three months mental health leave.
February 2005: Jack recruits Owen to Torchwood towards the end of his three months leave.
[Early] March 2005: DW 1.04, 1.05, Aliens of London/World War Three. Tosh goes to London posing as a doctor to investigate "space pig"; covering for Owen who had a hangover in his second week.
September 2005: DW 1.11, Boom Town. Jack keeps TW team under lockdown so that none of them run into his former self (from info in Twilight Streets). The TARDIS chameleon circuit creates a perception filter directly above the Torchwood Hub, which Jack subsequently uses to create the invisible lift.
December 2005: DW 2.0, The Christmas Invasion. Jack obtains (catches? steals from TW1?) the Doctor's severed hand.
Tosh and Owen snog out front of the Millennium Centre.
March/April 2006: DW 2.03 School Reunion. The Doctor and Sarah Jane (squee!) are briefly reunited.
June 2006: DW 2.12, 2.13, Army of Ghosts, Doomsday. Battle of Canary Wharf; Lisa Hallet semi-converted; Two members of TW3 go through the wreckage of TW1 (Owen and Suzie?); Ianto Jones seeks (and finds) employment at Torchwood Three.
July 2006: TW 1.01, Everything Changes, TW 1.02 Day One.
August 2006: TW 1.03, Ghost Machine, TW 1.04, Cyberwoman.
September 2006: TW 1.05 Small Worlds, TW 1.06 Countrycide, TW 1.07, Greeks Bearing Gifts. Approximately three years after Tosh started working for TW3 in 2003.
October 2006: TW 1.08, They Keep Killing Suzie, TW 1.09 Random Shoes.
December 2006: TW 1.10, Out of Time.
DW 3.0, The Runaway Bride.
January 2007: TW 1.11, Combat, TW 1.12, Captain Jack Harkness.
[Early] February 2007: TW 1.13, End of Days
DW 3.11, Utopia. Based on the persuasive arguments of lorannah, who suggested that the Doctor takes Martha back a few months before he met her in order to take advantage of the Rift activity caused in TW 1.13.
[Late] May 2007: DW 3.01, Smith and Jones, DW 3.06 The Lazarus Experiment.
June 2007: DW 3.07, 42 (Phone call to Martha's mother).
TW team are sent to the Himalayas. It is approximately 18 months since the downfall of Harriet Jones in The Christmas Invasion.
DW 3.12, DW 3.13, The Sound of Drums/Last of the Time Lords (Not counting the year that never was).
After LotL, Jack, Martha and the Doctor spend a few days resettling Martha's family and cleaning up the mess on the Valiant. During this time, the TW team return from the Himalayas and start hunting the Blowfish Alien.
TW 2.01, Kiss Kiss, Bang Bang.
July 2007: TW 2.02, Sleeper, TW 2.03 To the Last Man. (TTLM takes place on July 20th, the only viable "Friday 20th" in 2007).
August 2007: TW 2.04, Meat.
SJA 1.0, The Invasion of the Bane.
September 2007: SJA 1.01, 1.02, Revenge of the Slitheen*.
TW 2.05, Adam.
October 2007: SJA 1.03, 1.04 Eye of the Gorgon.
SJA 1.05, 1.06, The Warriors of Kudlak.
November 2007: TW 2.06, 2.07, 2.08, Reset, Dead Man Walking, A Day in the Death. (There is nothing definitive that places these TW episodes at these exact times; I just think that the spacing works well).
SJA 1.07, 1.08, Whatever Happened to Sarah Jane?.
December 2007: SJA 1.09, 1.10, The Lost Boy (Sarah Jane says it's been five months since Maria moved in/she adopted Luke).
DW 4.0, Voyage of the Damned.
February 2008: TW 2.09, Something Borrowed.
March 2008: TW 2.10, From Out of the Rain.
April 2008: TW 2.11, Adrift
May 2008: TW 2.12, 2.13, Fragments/Exit Wounds.
September 2008:TW Radio Play, Lost Souls (It has been "some time" since Tosh and Owen's funeral).
October 2008: DW 4.01, Partners in Crime.
DW 4.04, 4.05, The Sontaran Strategem/The Poison Sky (Donna's neighbour says she hasn't been seen for a "few days".)
DW 4.06, The Doctor's Daughter.
November 2008: DW 4.12, 4.13 The Stolen Earth/Journey's End.
*Someone needs to write me a fic where Jack and Ianto get trapped in the Hub when all the lights go out/all electrical technology stops working during Revenge of the Slitheen.