In particular I am looking for (I'm pretty sure it's TOS and a classic) fic where Jim is serving aboard a Vulcan vessel, bonded to Spock. Jim wears concealing clothing. He wears a mask. The crw thinks its because Kirk is beautiful, and in order to stay faithful to his mate he hides himself. None of the crew (except Spock and the Healer) know that Jim is actually a human. I think this was pre-Contact setting, and there's a barrier of some sort. A Fed ship does make it through and Jim knows some of the officers aboard and Spock uses Jim's knowledge of Standard to be able to communicate? I know after they meet up, Bones suggests to Jim that he might want to find a woman, years of being amongst aliens and all -- and Spock mentally pulls back, willing to let Kirk go if that is what he wishes. Kirk stays with his bondmate, content to be so.
Edit (thought of a few more things that might help narrow it down) : Jim was the only known human on Vulcan because of the barrier. Because he is human and looks "odd" to vulcans, his ability to sweat has him likened to a pale burrowing worm on Vulcan. This reminder is made again when Jim meets with the Federation ship's crew -- because he hasn't seen himself in years. He wonders how Spock can stand it, when he feels slightly nausiated by the sight of the humans -- his own species.
I believe he was also friends with a friend of Spock's who was a vulcan prostitute. It was normal for the society and he was willing to accomadate Jim as a friend, not as a duty. This person, or the healer, may have been the one to bring Jim to Spock when the other man went into pon farr but rejected any except for Jim.
Found!! http://archiveofourown.org/works/1600082 ~ Eye of the Beholder by raynewton.
There is also a sequel!! https://archiveofourown.org/works/1867161 ~ Second Contact by Fiona James
I also know there's a fic out there where something goes wrong on Enterprise. Something big to the point that Jim cannot and will not serve as her Captain. He feels the crew has betrayed him and requests and recieves a transfer to a Delphine (I think) class exploration vessel. He also meets two new crewmembers who become friends. I think an Alternate Alternate Enterprise pops up at some point and the small ship and her crew are distrustful of them -- because they are the same people that hurt *their* Captain.
Found!! http://www.fanfiction.net/s/10480306/1/Prologue ~ A New Start series
I will also take any story where Jim Kirk is on another ship -- even if it's just a brief secondment while Enterprise is doing refits. I prefer him with Spock, but I will also gladly take Spock!Prime.