-Anything on the ground SAFE
-necroplanes SAFE
-wasps SAFE (Cobra and Viper as well)
-megapol patrol SAFE - everything from Megapol is safe
???s:
-raiders? NOT SAFE
-gunboats? NOT SAFE
-military supply NOT SAFE - but I'd risk it anyway, since it carries decent loot (good armor for early-mid game)
-Those weird metallic things? NOT SAFE - that's a Small Scout type shipping
-Freighters? NOT SAFE
Some additions:
- any civilian shipping (obviously) is safe
- ambulances are safe, even though they are Academy faction (there is a scripted retal mission though)
- any 'Star God tech' shipping (steel colored vessels) is not safe
- all 'roving bands' is safe (though they might trigger a retaliation if they happen to pass close to your base)
- zombies - all ships flown by the zombie faction (including the normally not safe ones) are free game - Zombies don't do retaliations, or at least I've never seen one
- simply anything from Bandit, Zombie, Megapol, Civilian, Reticulan, Necropirate, Dark Ones factions is safe
- anything from major factions (+Humanists and Raiders) is not safe
- I have no idea about Spartans - never had a retal from them, but not sure if it was just luck - it would be safe to assume they can retal EDIT: Yes, they can crackdown.
- might not be obvious but Govt shipping is not safe - not only it carries a hefty penalty to score when shot down (Ordinator and Govt Fighter only), it can also trigger a retaliation. Landed ships are safe though, so if you have researched govt personnel and take care to stun a lot, landed Ordinators might be decent loot, if difficult to assault.
- mutant freighters, if you get that far, are obviously safe from retal, but again - carry a large penalty for shooting down. They carry plastasteel though, if you critically need it. Onb the other the infamy penalty for shooting down, assault and not completing the trade mission might be high enough to make you consider buying the p-steel instead.
- a vessel colour cheat sheet: white, green, blue and light brown is always safe. Steel and dark brown - not safe (most of the time).