Your Friend by flit_st_fanfic: A mission goes badly but Kirk won't tell Spock how, not really.
Guilty Until Proven Innocent by Gothraven89: WARNING non-con. Something horrible happens to Jim and it would be expected that his First officer along with the rest of his crew would be there for him. So much for expectations.Hurt!Kirk guilty Spock&Crew. K/S
All I Got For Chrismas Was A Roofie In My Drink by Zhen123: Bones and Jim spend their first Christmas as Cadets at a bar...where Jim is met with an unpleasant surprise. Bones is not pleased. Pre-slash.
Deja Vu by d8rkmessngr: The aliens got the wrong secrets from Jim Kirk.
Awesome, awesome fic, but NOT for the faint of heart.
Standby by d8rkmessngr: He was glad Bones was dating again. He was. Really. But what Jim thought was good for Bones turned out to be oh, so wrong for Jim.
The Seemingly Dubious Nature of Your Answer by vampiric_mcd: Five times he said no and they didn’t listen – one time he said yes and they did.
Yeah, this one stuck in my head, largely because of Winona's role in it.