An Abbey world map location north of Gecko, featuring monks hoarding pre-War wisdom. This is also where the PC would have run into Ian, still alive after 80 years (but killed in Necropolis according to the Vault Dweller's memoirs).
A village outside Vault City, whose inhabitants are trying to avoid being turned into "servants".
Presumably this is what Myron alludes to when he mentions pre-War bases.
A Shi quest tied in to the EPA, related to the ending where the Shi get attacked by a sentient plant.
The interior of the Hubologist space shuttle (accessible from San Francisco map with keyboard and with CTRL-R) and three endings where the Hubologists kill themselves in different ways by means of the shuttle .
A second part of the Help Lara attack Tyler's gang quest where the player would go with Lara's gang to the party Tyler is attending and fight him and the remains of his gang.
Putting the kids in the Den in an orphanage (possibly run by Mom), with the beneficial side effect of the player not having to risk being pickpocketed any more. Also killing Metzger and telling Karl to return to Modoc should have had quest entries.
Diplomatic characters would have been able to beat the raiders by talking to Shadow-Who-Walks and making him leave their employ (Shadow-Who-Walks had been planned to be Sulik's archenemy).
A good ending for the deathclaws of Vault 13, where the Pack expands peacefully into the surrounding territory. According to John Deiley, who designed Vault 13, this was scrapped because the Enclave plot required the slaughter of the deathclaws. Killap's unofficial patch gets around this by a simple solution: killing Dr. Schreber in Navarro saves the deathclaws if the player can kill him before the attack (two weeks after first entering V13).
Good endings for Vault City and Gecko. The good ending for Gecko which revolves around Gordon's "greed is good" scheme is only inaccessible because of a bug.
Two Vault City endings where Vault City is razed and one Gecko ending where Vault City invades Gecko.