Kharak being destroyed and this music playing was probably one of the most 'emotional' experiences a game has ever given to me.
http://www.youtube.com/watch?v=fXRJBK8oJSA
Homeworld had some absolutely amazing mods too, but... that game lacked intimacy.
Not much in the way of 'upgrades' or crews or captions or personalities or heroes to get attached to. Each ship was pretty much 'just another ship'
Ground Control was pretty neat, and very Mechcommander-esque. I much prefer that style of RTS. Instead of just massing gigantic armies and spamming them into combat until your enemy is overwhelmed, I prefer the more 'squad' orientated game. You start with your small, but elite forces, you can't really get MORE of them, you have to work with what you have.
Jagged Alliance 2 (and the mods for that game) were AMAZING.