The following is canon in my head! And it will remain that way even if until proven otherwise by real canon. (Spoilers for Doctor Who season 5 and minor spoilers for Torchwood season 4.)
In my personal head canon of the Doctor Who / Torchwood universe:
* Rory Williams is a relative of Rhys Williams, though they're not exactly close. Rory missed Rhys and Gwen's wedding because he was working / studying for his exams. Rhys missed Rory's wedding because of the baby. They will meet up again one day and, after a series of odd events and revelations about each other, have a good laugh about how weird their lives are. Gwen and Amy will get along but don't really keep in touch, both being a bit more preoccupied with other things and their own adventurous lives. Since Jack never really talked to Gwen about The Doctor, Gwen will ask Amy a lot of questions about him and she’ll be more than happy to fill her in on everything.
* Gwen Cooper and Ianto Jones are (were) BFFs. They made out while Jack was gone between s1/2 but it didn't go anywhere. Jack is unnerved by how well they get along -- and they know it and play it up to purposefully annoy him. Jack wants a threesome; the other two were secretly open to it, but the circumstances just never happened.
* In his parallel universe, Ten II has pretty much taken over running Torchwood. He wants kids but Rose doesn't, at least not yet. He wants that whole domestic happy family life. (Like the one he gave up from being John Smith -- you know, in that episode where Martha was subjugated to horrible racism and servitude.) He runs Torchwood sort of mostly to impress Rose.
* Death results in a shift of life energy to the/a void, like another dimension or parallel space; Adam talked about death being the void, so I'm going with it. This is the "darkness," but it's also "dark" because of the inability to see (physical eyes required) or to form physical memories in the brain while disconnected from the body. There is more out there, but it's not like any religious claims and it can't be comprehended/remembered by the mass of energy experiencing it.
(I actually intended to do a whole write-up about the philosophy of death in Torchwood and the new Doctor who, but I haven't gotten around to it mostly because of all the work it would need. I hold the right to change my opinion on this if my future research leads me to a different conclusion. If you know of any analyses of this already, please let me know.)
* Owen Harper is not dead; it took him a while to figure it out, but he is a disembodied mass of energy lurking around our world, thanks to the glove. This frustrates him greatly because he still makes snide remarks at Jack's leadership qualities, but he can't piss Jack off with them because Jack can't hear him. This was especially annoying for him during the agonizing (for Owen) events of Children of Earth when he had to watch everything fall to shit and couldn’t help or mock them. Possibly taking it a step further (I’m undecided on this), Owen is the one who triggered the defense mechanism to protect Gwen and Ianto during the events of The Stolen Earth. He triggered them again to limit the blast size in CoE.
* Jack Harkness is capable of sharing his life energy and bringing people back to life. It's similar to how Suzie and Gwen shared energy from the glove which healed Suzie, the difference being that Jack won't die from the energy share -- though he might still suffer some pains from the other person's wounds before healing. This is hinted at with his Kisses of Life in the show, but can be extended to fully bringing people back to life long after death. Jack doesn't know he can share his energy to this extent, or how to do it if he did. By the time he does figure out he can do this, (a thousand years? a million?) he will probably be accepting of death and unwilling to use it except in extreme cases. (Such as saving the cat-nurse when New^15 New York was hit with a virus. And yes, Jack Harkness is the Face of Boe in my head canon, too.)
* Suzie Costello is not a psychopath/sociopath or afflicted with antisocial personality disorder. She is very capable of emotion and emotional ties, and it's genuine. She's also extremely disturbed from her childhood, highly intelligent, and a workaholic, and under the stress and isolation caused by Torchwood this adds up to her behavior. This is why she couldn’t shoot Gwen and chose to shoot herself instead. She shot Jack (her stress-causing boss!) partly because he’s a bastard, but also because something happened before in the field and she suspected he could recover from serious injury or death and was angry or possibly jealous, or maybe just pissed for not opening up to her. (If Owen had been there she might have unloaded the clip into him.) She really did go to those meetings because she needed to talk. She is also paranoid and despite her desires to be open with others, she finds it difficult to trust; the behavioral triggers were in case she was retconned or locked up, not in case she died. She is also totally coming back to life again, you guys.
* Gwen is a reincarnation of
Gwyneth. She has survived Torchwood in part due to her latent/subconscious psychic/clairvoyant abilities, which Gwyneth also had. Gwyneth's abilities somewhat made her mad/miserable/led-to-her-death, so in her reincarnated state (which Gwyneth triggered herself) the abilities are more subtle. This is why Gwen was able to fight off the effects of the retcon in episode one. This also contributes to why Gwen is a good police constable and an influential leader, why she can get almost anyone to open up to her, and why she's so afflicted with empathy.
* Whenever/wherever Amy and Rory settle down after traveling with The Doctor, they will keep in touch with River Song. Mostly because Amy likes her. (Not like that... well, maybe like that. :D)
* River Song is from the planet “Awesome” in the “Kick-Ass” system, part of the “BAMF” quadrant.
Okay, that’s it! What’s your head-canon, flist?!