I can never decide what to put in the first place: WC1, WC2 or Privateer.
I think my list goes something like this (with the top three positions being very close to each other):
1. WC1 (great story, great atmosphere, medals, promotions, great manual, blueprints...as perfect a game I have ever played)
2. WC2 (good story, my favourite Confed ship the Rapier II G, and coolest of all: speech!)
3. Privateer (just great fun with a good story and in its simplicity it had great depth, like e.g. the scanner upgrades)
4. SM2 (flying a Dralthi!)
5. SO2 (flying a Morningstar and meeting Maniac again!)
6. SO1 (capturing Thrakhath!)
7. SM (great ending cutscene, great atmosphere)
8. RF (it's always fun to shoot Retros)
9. SOPS(it was cool to see the aging Excalibur and Thunderbolt next to the top notch fighters. Much better story telling and atmosphere than in Prophecy)
10. Prophecy (atmosphere and story were awful when compared to most WC games but the gameplay really was fun)
11. WC4 (very cool interactive movie)
12. Academy (I spent countless hours building my own campaigns and great manual)
13. Armada (flying for the Kilrathi!)
14. WC3 (too radical a cut with the former games I thought and the least likeable cast of characters in any WC game. And boo for destroying Kilrah.)
16. Priv2 (weird story and setting and cool ship designs)
16. Arena (sorry Arena: you're a great little game with an awesome manual but the competition is just too stiff)
Just like LOAF said: it really does not mean that I don't like Arena or Priv2. But in a game series of awesomness they're just a little less awesome than the rest.
Sadly. I still haven't played SWC