(Operation: Anchorage, The guns of Anchorage quest) The paratrooper with a gauss rifle will be Elijah from Dead Money. There will be two crimson dragoons dressed as ghost people.
The firelance encounter is removed, and the alien blaster in the New Vegas encounter is replaced with the firelance.
If you attempt to use the NCR emergency radio in the CW, an NCR trooper may run up a day later, and report in to you, before dying of starvation. It is not possible to save him. If you use it in Operation Anchorage, he may materialise in, before an error sound plays and he dies. His dead body will be found outside the pod. If used in mothership zeta, he can be found in one of the rooms being studied (haven't played zeta yet, so not sure).
This holotape: http://fallout.wikia.com/wiki/Private_contract will have 'head' replaced with 'booty' and the cap amount increased extremely (e.g. 347823478).
(Random location) A dead cazadore with a sign saying 'I thought we were safe!'. (Referring to how cazadores aren't in fallout 3)
(Random location) An undamageable raider with what appears to be a .32 pistol. He will attempt to shoot it, but it will make a clicking sound. He will then question where his ammo was, and then will simply disappear using the Operation: Anchorage animation, leaving the special '.32 pistol' which is a misc item and can be sold for 32 caps.
There will be a pulowski shelter with a skeleton named 'christine' in it, with an explosive collar.