This is not a comprehensive list, but it's most of the big things, in no particular order. (First two are kind of long, sorry.) There are spoilers for the whole season, of course.
1. The Jack/Gwen/Rhys triangle and all its angles.
Gwen/Rhys
Last season, I would not have believed that Rhys was going to live through another season or that Rhys and Gwen's relationship would survive. But it did survive, and I really believe that they both love each other, and indeed they actually succeeded in getting married. Their relationship was given ordinary conflict and depth and feels *real*. That helps me relax a bit and believe that the Gwen/Rhys relationship is considered vital to the series because Gwen's Normal Life is a cornerstone of the series.
(Although obviously it's setting myself up for a fall, to believe anything is "safe" - I certainly wouldn't have thought they'd kill one of the main characters in the middle of a season, then kill him AGAIN plus ANOTHER main character.)
Jack/Gwen
Last season, I saw their relationship as a fairly intimate, platonic one, and I really really wanted it to stay that way. Bad things happen when UST gets out of hand or becomes RST, right? But I was impressed with how they handled that in s2. There was blatant UST, but we also got to see how much respect Jack has for Gwen's relationship with Rhys, which is of course related to the way he feels about her Normal Life. Jack cares about Gwen in a special way (guh, I LOVED the way he gently lowered her sleepy head onto the table in "Adam") but he wants what's best for her, because what's best for her is also best for him and the others. And a fully-realized romantic relationship with Jack is not what's best for Gwen.
So Gwen gets the best of both worlds (if there can really be any "best" about Torchwood): an exciting man and the action life, and a sweet loving man and the normal life, and she doesn't even have to feel guilty. (Since apparently her infidelity from last season was erased by the Rift... sorry, this is the post about what I liked. Right.)
Jack & Rhys
It was such a great move to have Rhys find out about Torchwood. Not just because it meant Gwen could stop lying and start to work on a fully honest relationship with Rhys, but because we got to have Jack having naughty thoughts about Rhys (or joking about it anyway, it's the same to me) and Rhys being Rhys and rolling with the punches. If he's threatened by Jack, he's mature enough to see and believe that it's him that Gwen comes home to, and accept it at that. And Jack knows how important Rhys is to Gwen and I think he can see that he's a really good guy. I'd actually like to see more Jack/Rhys interaction, because aww, and the camaraderie of two people who love the same person can be kind of special.
And on a more specific note - the scene in "Meat" where Rhys confronts Gwen (or is it vice versa/both?) in their flat and they both get very angry and shout... GUH. Loved it. It was thoroughly well acted, and Eve Myles's accent got extra thick and that always turns me on. /shallow
2. Toshiko's death. That sounds terrible, but I don't mean the fact that she died or that she suffered. I care about that; in fact, I just made myself cry thinking about it on the way to work this morning, and I don't think I've done that in months. Although, to be fair, a spaghetti jar label also made me cry today, so, you know. ::headdesk::
I just mean... it was a good death. She died helping save the world the way she was always doing: in an absolutely essential support role. It wasn't as flashy as physically pushing the buttons to stop the nuclear disaster, but Owen wouldn't have known what to do without her. And with the relationship, the character interaction, it was the same thing: she stayed in the background, didn't make it about her, just supported Owen, and I find that strong and sacrificial. I tell you what, if I had been shot in the stomach, dragged myself down a flight of stairs, and was dying alone, I would sure as heck TELL the only person I had contact with. I would want some comfort and sympathy! But she wanted things to be easier for Owen, not sadder, so she kept herself out of it except to help him focus. ("You're breaking my heart!" Not - "I'm going to die too!")
(I've seen other people mention that if the writers weren't going to do anything more with her character, then it was nice she at least got a good death. I can see that. I was frustrated that the character had so much potential, but the only thing the stories seemed to be able to focus on was Tech Whiz - sometimes - or Sad Romantic Failure - more often.)
Also, as disturbing as it is, the image of her dragging herself down the autopsy room steps to get to her scanner, so she can help Owen with the nuclear plant, has become iconic to me. It's on a very short list of things where I can say to myself, "This situation I'm in is hard, and I don't think I can do it, but if Tosh could force herself to get down those steps with a bullet in her stomach..." I know it sounds cheesy, but it really works for me, because the fictional comparison I'm using felt powerful enough to be real to me.
3. Showing us Jack cares about his team. I was not able to establish that fact conclusively in Series 1. (I talked about it more, and why it mattered so much to me, in the second half of
this entry. Emphasis on that scene near the end of "Adam," with all the staff in the board room: that was the thesis statement of the season, thematically and for all the characters individually and in their relationships with Jack. (I should really make a separate item for that scene in "Adam" but I need to get this post out of my head sooner.)
4. Character backstories. This is the only thing on my pre-season 2 wishlist that I didn't end up feeling cheated on - in fact, I got more than even thought to wish for, with Myfanwy thrown in! And I felt like they tied in the backstories - Tosh's and Owen's at least - with the theme of Jack caring for his team. He had rescued Tosh, he (in a way) had rescued Owen.
5. Vintage Torchwood. Particularly the lesbian dominatrices. No, not just them - all of the characters and all the scenes we saw. Torchwood has been around for a long time and there have to be so many interesting stories hidden there. Want. Some of them even have nothing to do with Jack!
6. "Adrift." There were things that either didn't make sense or made me want to smack Jack upside the head, but that aside, it was beautiful. Gorgeous cinematography and music, good acting, intensely sad, lyrical story, Ruth Jones (::love::), just a great atmospheric standalone story. One of their best, in my opinion.
I have one more post, and it's all about Owen.