You can gain reputation with the denizens of Shattrath’s Lower City by doing one-time and repeatable quests, and by killing monsters in three wings of Auchindoun.
The repeatable quest "Outcast's Plight" requires you to turn in 30 Arakkoa Feathers to an NPC located in Lower City. This quest is repeatable through Friendly.
You can also run Auchenai Crypts and Sethekk Halls, two wings of Auchindoun, to get through Friendly reputation.
There are many quests in Terokkar Forest and Auchindoun that grant reputation with Lower City. For the most efficient use of these quests, it is best to save them until you reach Honored.
Shadow Labyrinth, the final wing of Auchindoun, will grant reputation through Exalted on both normal and Heroic mode, as will Heroic Auchenai Crypts and Heroic Sethekk Halls. Doing these instances will be the only way to finish the climb to Exalted.