OK this will be the bare bones I can think of until I have the time/connection to take the dive:
Graphics:
In-game
Geometry
Hardware Transformation & Lighting (OGL/DirectX 8)
LODs*
Superdetail boxes (distance based subobject rendering)
Skyglobes/Skyboxes
Texture Formats
TGA, JPEG support as textures, ANIs as textures
'32-bit PCX' support (each PCX has its own palette)
DDS support
EFF container format to replace ANIs
Mapping
Diffuse mapping*
Glow mapping
Specular mapping
Environmental mapping
Mipmapping
Particles
Advanced Particle Rendering
Particle Based Thrusters
Lensflares
Interface
PCX-32 support
Scene design support
Sound:
OGG support
OpenAl implementation
Simulated Speech
Gameplay:
Dumbfire Indicator
Strafing enabled/mappable for players
Orbradar
Fighterbeams, Ballistic Primaries, Swarm, SSM, .... and more weapon modes
Design/FREDing:
MOD-support
AVI-cutscene support
Dynamic Tables
Multispecies support
Multiship Docking
Permanent Variables
Gazillion of FRED Sexp additions