Tactile Species - https://www.fanfiction.net/s/6956506/1/Tactile-Species This one is Kirk/Spock pairing as I remember so hope you don't mind slashy cuddles. :D Oh hell, everything I rec will be slash, who am I kidding!

Home - http://archiveofourown.org/works/292045/chapters/467224 This one has Jim struggling under the weight of depression and isolation and the responsibilty of the Enterprise.

There are a few more I can't find atm so I'll raid my terrifyingly extensive A03 and KSA history and come back to you with more when I find them.