In Home (4x03), on the mountain with his old girlfriend, Archer says he marooned a ship full of people and tortured someone. ERIKA: You did what any captain would have done. ARCHER: Does that include torture? Or marooning a ship full of innocent people? Because I don't remember reading those chapters in the handbook I assume the person he tortured is the one that he put in an air lock but when did he maroon a "ship full of innocent people"?
"Marooning a ship full of innocent people?" is a reference to Damage (Episode 3x19)
With a boarding party, Archer, and Trip transport onto the vessel, and manage to steal their warp coil while leaving behind three containers of trellium-D as well as other supplies in 'compensation'. When the Captain asks why Archer is doing this, Archer simply states that he has no choice before leaving, knowing that by taking their warp coil the alien crew has been left stranded three years from their home.
"Does that include torture?" is a reference to Anomaly (Episode 3x02)
Archer enters the brig and, holding a phase pistol to Orgoth's neck, escorts him to the airlock, startling some of the crewmembers on the way. Shoving him into the airlock, Orgoth refuses to respond, still thinking Archer is too civilized. Archer starts to decompress the airlock, saying that if he doesn't talk, he has less than forty seconds to live...Realizing that Archer wasn't bluffing, Orgoth says he'll give Archer the information he needs.