Let's try to make a comprehensive list of items that can be modded on the server that affects players without them having to get a download.
Unit Modifications
Unit speed, health
jet fuel modifications
collision modification (units can leap and not get hurt)
disable weapons
weapon damage
Mission Modifications
Increase/Decrease Height Limit (will cause jumpiness if player does not have new mission)
Spawn called units on different sides (player must load same units)
team death match mode
call two maps that the player already has (overlay/underlay of maps)
call new deathregions/remove deathregions specified in map
change spawn time
Map Modifications
No Capture CP (Hex edit or remove capture regions)
New Spawn Locations
AI Behavior (Hint nodes) e.g. placing mines
Wall collision removal (walk through walls)
Invisible wall addition (players cant see the new walls)
No Vehicles (by hexedit, presumable also by vehicle spawn point removal)
Give cps to the other team or make neutral
Add new deathregions (needs mission mod)
Common.lvl Modifications
grenade effects such as push
turret blast radius
health bot and ammo bot (change speed and/or take away health and ammo)
Zoom Values for weapons can also be override server side. (Random fact.)
Excellent thread I will try to add more to it later. I would suggest also putting the ODF/LUA code command next to each modification description so modders have an easy list for reference.
For units and weapons the client can load custom mesh and tga (e.g. if you change the rebel pilot mesh with an alien bith it will be online compatible.