From newest to oldest:
Ain't No Grave - When John Winchester wakes up to a post-apocalypse future, he only wants to know two things: where are his sons, and just what brought him back? AU in which the apocalypse ended a little differently, Castiel stayed human, and society suffered quite a bit more than it did on the show. Also available as a podfic, read by greeniron.
This Bitter Earth - Crossover with Criminal Minds. The Winchesters and the FBI's Behavioral Analysis Unit investigate the same case, a series of mysterious deaths on the grounds of a South Carolina plantation. Set late in the 4th season for both shows, but specifically after "On the Head of a Pin" in the SPN timeline. Also available as a podfic, read by waiting4rain42. (Includes m4b, m4a, wma, and mp3 formats.)
Highway Chile - While investigating a series of apparent drownings, Dean gets reacquainted with his old friend, Murphy's Law. Stanford-era solo hunt.
Stars Like Spilled Salt – Barely healed from their encounter with Meg's daevas, Sam and Dean take the case of a phantom funeral in southwestern Illinois. Set between "Shadow" and "Hell House."
Hear This Prayer for Her – The brothers' investigation of a haunted cemetery reveals a 150-year-old tragedy; a worn-down Dean may become the spirit's next victim. Set between "Born Under a Bad Sign" and "Tall Tales."
Torch Song – Children are disappearing in Durango, Colorado. Dean starts to take the case a bit too personally. Set early second season, between "Children Shouldn’t Play With Dead Things" and "Simon Said."
The Wind Remembers Their Names – The boys look into a series of mysterious hypothermia deaths in small-town South Dakota. Set after "Jus In Bello."
Tango Papa Romeo Sierra – Sam and Dean investigate a haunting at the National Museum of the U.S. Air Force. Set early season 3.