These are a few of the mods which have obvious influences on Fallout 4.
Wasteland Defense
WMX Weapon Mods
Project Nevada's enhanced visions
Alternate Repair
The companions and settlers seem to borrow concepts from various follower overhaul mods from FO3 and FNV such as using weapons and gear assigned to them instead of just what is the most powerful.
Robco Certified
Has anyone else come across aspects of the game that were clearly influenced by from mods that you used?