Angel - Explosive
Blood - Thermal
Drones - EM
Gurista - Kinetic
Mercenaries - Thermal
Mordus - Thermal & Kinetic
Sansha - EM & Thermal

Damage Types Dealt by NPCs:
Ammatar Navy - EM/Thermal
Amarr Navy - EM/Thermal
Angel Cartel - All Types
Blood Raider - Thermal/EM
Caldari - Kinetic/Thermal
Gallente - Kinetic/Thermal
Guristas - Kinetic/Thermal
Minmatar Fleet - Thermal/Explosive
Mercenaries - Kinetic/Thermal/Explosive
Mordu's Legion - EM/Kinetic/Thermal
Rogue Drones - All Damage Types
Sansha's Nation - EM/Thermal
Serpentis - Kinetic/Thermal
EOM - EM

-Smallest to Largest Site
Burrow > Hideaway > Refuge > Rally Point > Den > Yard > Port > Hub > Haven > Sanctum