Spoilers: Through "Moebius 2," the last episode aired in the US. None for S9.
Note: Title from "Miracle Drug," by U2. Transcript help from Solutions Wiki
Science and the Human Heart
"I knew I'd like you." This first real Sam/Daniel moment, from the very first episode of Stargate SG-1, really sums everything up. Sam and Daniel's relationship is often an effortless blending of people alike in passion and interests, scientists with complementary points of view, two lifelong lovers of knowledge who also love each other very much, regardless of whether that love is platonic or not.
Daniel Jackson is, in brief -- an anthropologist/archaeologist/all-purpose social scientist, a husband in the first three seasons, a widower since S3, an orphan, a scientist and scholar who's learned to live with and fight side by side with soldiers, and a life-long quester after knowledge. He is passionate about the things that matter to him -- finding his wife, finding and protecting his wife's son Shifu, and protecting the universe's innocents and its collected knowledge. His guardian race is the Ascended/Ancients, one of whom, Oma Desala, helped him to ascend at the end of S5 when he was dying of radiation poisoning. He returned to this plane of existence at the beginning of S7, changed by the experience -- a bit stronger, a bit more action-prone and less ponderous. At the end of S8, in "Threads," he discovers more about the Ancients and about Oma, and realizes that his need to intervene, to take action, is stronger than his desire to acquire the knowledge of the Ancients. Daniel's life is a struggle between these two urges, between the active and the contemplative life. His love of knowledge and need for precise and accurate data balances out his tendency to rush in where everyone else fears to tread.
Sam Carter is a military brat, the daughter of General Jacob Carter, and is lifetime Air Force -- at least in this reality. She's very conscious of her role as a woman in a man's world, and especially early on, felt like she had to prove that she was just as tough as any man she met. But Sam's military toughness is balanced by a maternal streak, displayed in her relationship with Janet's adopted daughter Cassie, and while she's military, she's not necessarily militaristic. Sam is passionate about science -- her field is theoretical astrophysics, and she was part of the team that got the Stargate working in the first place so many years ago. Like Daniel's, Sam's theoretical knowledge has lost some of its edge because of all the time she's spent in the field, but she's still one of the leaders in her field. Occasionally, Sam's fascination with the universe's physical phenomena interferes with her humanity -- as in "A Matter of Time," when watching a blackhole in action is so exciting that she doesn't see, as Jack does, that she's watching people dying. For the past couple of years, Sam has been struggling with finding a balance between the work she loves and the possibility of a personal life. She had a serious relationship with a cop named Pete, and was engaged to him for several months, but she eventually broke up with him because of her feelings for Jack.
Okay, okay, so it's canon. Sam has feelings for Jack. But Sam and Daniel are meant to be.
Sam and Daniel's friendship, based not only common interests but on a shared passion for knowledge, is one of the least problematic relationships on the series. There is no episode that's about their friendship, the way "Shades of Grey" is about Jack and Daniel's or "Divide and Conquer" is about Jack and Sam's. But they are friends, and always has been.
In "Children of the Gods," Daniel shows Sam the cartouche he discovers and tells her his theory about why the Stargate addresses he found don't work. Sam grins and says, "I knew I'd like you," then confirms his theory, explaining about stellar drift. There are many other examples of the two working together, their specialties complementing each other. It happens in "Thor's Chariot," where the two of them together demonstrate the knowledge and sophistication that proves their's is a mature civilization. In "Serpent's Venom," they work together to booby-trap a bomb. As the seasons go by and physical strength and cunning become more important than scientific ability, Sam and Daniel continue to work together well, as we have seen in season 8, with such things as "Covenant" springing to mind as examples. In fandom, they're often called the science twins because of the way they work together, but their relationship isn't just professional.
We are only given glimpses of the many talks they have, but it seems that, on missions and at the SGC, they talk a lot. In S1, Sam asks Daniel about his wife -- though she's horrified to learn Sha're was a gift -- and comes to respect the deep love Daniel has for her. In "Need," it's Sam who reminds Daniel that he shouldn't marry Shyla because he already has a wife, and in "Forever in a Day," Daniel's vision includes a moment in which he tells Sam what he admired most about Sha're -- her sense of wonder.
Early on, Daniel's credulity surprises Sam -- in "Thor's Hammer," he doesn't understand why he puts his trust in Kendra, and he tells her he just has a feeling that Kendra is honest. Sam isn't used to using her intuition; it's not a trait valued in the life she's led up till now. But later in that same season, in "Singularity," Sam stays with Cassie because of a feeling she has, and because of the feelings she has for Cassie. It's not just because of Daniel that Sam learns to be more open -- but Daniel has a lot to do with it. A conversation between the two in "Singularity" is a perfect example:
Sam: I know I'm supposed to be detached.
Daniel: Who said that?
Carter: Sometimes I forget you're not military.
In fact, all of "Singularity" is a perfect demonstration of how much Daniel cares for Sam and of the tentative understanding that is growing between them.
Four years later, at Daniel's deathbed, Sam says, of Jonas, "He stole some naquadria for us. He took a big risk, he said it was because of what you did. I think it could be important and I wanted you to know that. You have an effect on people, Daniel. The way you look at things, it changed me too. I see what really matters. I don't know why we wait to tell people how we really feel. I guess I hoped that you always knew." Sam's reaction to Daniel's death in "Revelations" is open and emotional; she sits in Daniel's office remembering him, and she longs for others to share her way of grieving. There's never any doubt that Sam truly does love Daniel.
It's a pity that Sam and Daniel's friendship so often gets overlooked, both in canon and in fandom, in favor of the two big, dramatic relationships on the show. The unresolved romantic tension between Jack and Sam, the tenuous and charged friendship between Jack and Daniel -- I tolerate the first and adore the second, but the charge between Sam and Daniel is subtle and explosive, fascinating in part because it's so often overlooked.
In fact, it was "Fallen" that convinced me, particularly the part of "Fallen" when Sam tells Daniel that no, there was never anything between them -- they were just really good friends. Until then, I was basically a slasher with some sympathy for Sam/Daniel shippers, but with that denial... well, it upset me. And I realized over the course of S7 that I really, really liked Sam and Daniel together, loved their friendship, loved, even, the fact that amnesiac Daniel wondered if there had been something between them. And I love the scene in "Orpheus" where they're working out together and discussing a movie they've seen.
It's often pointed out that even in the AUs, Jack and Sam are Meant To Be. But in two of my favorite AUs, "2010" and "Moebius" (also known as the Dorkverse), the chemistry between Sam and Daniel remains intact. They're obviously close friends in "2010," even many years after the Stargate project disbands, and friendly enough for Sam to kiss Daniel's cheek. And in the Dorkverse, their meeting with each other inspires an instant fellowship, right down to the matching glasses. "Moebius," of course, contains another canonical denial, where dorkverse!Sam tells dorkverse!Jack that she actually likes Daniel -- then takes it back a few minutes later, saying she was lying.
My love for Sam/Daniel is something of a philosophy, because it's related to my belief that best friends make the best lovers. Sam and Daniel are close friends, no one can deny that, and they understand each other professionally and personally. They enjoy talking together, enjoy working together, enjoy each other's company. They provide comfort and sympathy and love, they grieve for each other. Many people will tell you that pairing them is incestuous, not literally, but metaphorically -- their closeness and similarity is that of a brother and sister, not lovers. People will tell you that getting involved with your best friend ruins the friendship.
But romance, especially long haul romance, is a partnership between equals, and Sam and Daniel's partnership, as colleagues and friends, has been tested by blood and grief and death, and it remains strong at the end of eight years. I imagine it will only grow stronger.
A Word or Three on the Fandom:
This is one of the most varied fandoms I've seen. Fans of the pairing range from those who find it "really sweet" to those who find it "really hot." I'm noticing a lot of overlap with the OT3 and One True Team crowd, but there are lots of people for whom this is a one true pairing. There aren't a lot of people who will write this before "Forever in a Day," but we write it at just about every point afterwords.
I've included links to both older and newer archives, and I think you'll find that as time has passed, the fandom has changed a lot. But you'll find a huge amount of variety, fic cute and fluffy, intense and angsty, painfully dark, and brutally hot. I hope you'll join us.
Statistical Outliers, old archive
Scientific Minds, the new archive (G-R only) [seems to be down tonight, June 3, 2005. Azar, what's up?]
"Statistical Outliers" by Christina Kamnikar, the seminal Sam/Daniel fic.
untitled ficlet by dirty_diana
Unreasonable by raqs
Ghosts of Christmas Past by seimaisin
Cold Coffee by Raven
While He Was Gone by Juliette Torres (not strictly Sam/Daniel so much as Jack/Daniel UST with Sam/Daniel sex, but dammit, I liked this fic a lot when I read it a couple of years ago.)
Salvage by sage_theory
Cagey's fic, all of which is good.
Other Fic Recs (since mine are woefully inadequate):
surreallis recs Sam/Daniel smut (mostly newer, LJ-based stuff)
versaphile recs Sam/Daniel of all varieties (hasn't been updated in awhile, so mostly older stuff.)
Callea Veda's vids (and other Sam/Danielish content)
(Sadly, some of the best vidders in the fandom seem to have gone on permanent hiatus, and their vids have gone missing. (*cough* Wistful *cough*)