However, I'm currently undecided on a few names.
In scenes from Teyla's viewpoint: Teyla, I feel, would think of herself as "Teyla", Ronon as "Ronon", Sheppard as "John," and McKay as "Rodney." However, even in season five, we sometimes hear her call Sheppard "Colonel Sheppard," so am I wrong here? What about stories set in earlier seasons? Should she actually think of Sheppard as "Colonel Sheppard" until Conversion, when he tells her to call him John? How would she think of Woolsey? I'm thinking a nice, respectful "Mr. Woolsey", perhaps?
In scenes from Ronon's viewpoint: I think Ronon's simple: surnames all the way. He's "Ronon," Teyla's "Teyla", but it's "Sheppard," "McKay," "Weir," "Woolsey," "Beckett", "Keller" etc. We've never heard Ronon call Sheppard anything other than "Sheppard", have we? (Well, except for things like "buddy" etc., but that's a dialogue thing, not a narrative thing.)
In scenes from McKay's viewpoint: I imagine that he thinks of himself as "Rodney", and thinks of Sheppard as "Sheppard" (even though he might sometimes say "John" in dialogue, when hard pressed) - although in stories set in season one, he might think of Sheppard as "the major", since that's often how he talks about him then. It would be "Ronon" and "Teyla", since when are those characters called anything else? Woolsey would be "Woolsey." Weir...? Probably "Elizabeth" (although he does call her "Weir" quite often) and Carter "Sam." Carson? Well, they are friends, but we do fairly often hear McKay talk about him as "Beckett". Still, I'd probably go for "Carson" here. Keller...? "Keller" at first, probably, then "Jennifer" in stories set later in season five.
In scenes from Sheppard's viewpoint: Sheppard actually troubles me most. I've always called him "Sheppard" in scenes from his viewpoint, but I've been deliberately trying to change that to "John" in the last few months, since we've several times heard him talk to himself, calling himself "John," so I think he probably does think of himself as "John."** As with everyone else, "Ronon" and "Teyla" are easy. McKay...? In dialogue, he calls McKay "McKay" and "Rodney", fairly interchangably, but how does he think of McKay? I tend to use "McKay" in narrative from Sheppard's viewpoint, but "Rodney" in actual dialogue, but I'm still not confident about this.
* Though this is just my way of writing, and other authors use other approaches. I'm not setting up my method as the only way, just trying to make sure that I use names consistently and correctly within the rules that I've set for myself.
** Though, really, how often do we think of ourselves by name? That's why in my slave story, Slave Sheppard had never come up with a name for himself, since you don't need a name in your own internal thought processes. A name is something needed by other people, to distinguish you from someone else.