Walkabout by cofax
Stargate SG-1 | Season 9 AU | Short stories, complete

After Earth is conquered, Jack searches the galaxy for other refugees.

Walked Right Out of the Machinery by rydra_wong
Stargate SG-1 | Season 6 | Novel, complete

Jack's blending with Kanan goes wrong in a whole different way.

General Jack: Year One | Year Two | Year Three | Year Four by Flatkatsi
Stargate SG-1 | Season 7+ AU | Novel series, WIP

After a surprise attack injures General Hammond, Jack finds himself unexpectedly promoted.

Living Lives of Quiet Desperation by Sideshow Seryn
Stargate SG-1 | Seasons 2 Through 5 AU | Long novel, complete

A wormhole accident on an early mission leaves Jack marooned with a severe brain injury, creating dramatic changes to the timeline.

The Knife's Edge of Madness by Strix Varia
Stargate SG-1 | Season 5 | Novelette, complete

Alternate ending to "Desperate Measures"; Sam escapes on her own, but before she can get back to the SGC she's caught in a terrible accident.

A Trip to St Elsewhere by MB
Stargate SG-1 | AU | Short, complete

Janet Fraiser can't help but become attached to one particular patient.