The Ur-Quan and The Words. It always seemed nonsensical to me that The Words ("Hold! What you are doing to us is wrong. Why do you do this thing?") would affect the Ur-Quan so strongly, when a similar phrase ("Why do you wish to enslave us?") doesn't do anything. Then it hit me: the Ur-Quan (both Kohr-Ah and Kzer-Za) know, deep down, that what they are doing is unjust and unreasonable. The Words are a direct challenge to their ideals, and force them to confront this fact. The Words make them feel guilty, and their subsequent explanation is as much them trying to justify their actions to themselves as to the speaker of The Words. A simple question does not hold the same challenge, which is why they don't react to it. -Dark Hunter
Also remember that the Ur-Quan have a racial genetic memory, they talk about their ancestors howling in the chambers in their mind when you have the Dnyarri in your cargo hold for example. By repeating the very first words that ever gave them pause, spoken by their friends, you're triggering the memories of thousands of years ago, making them see you as ancient friends, instead of just another sentient begging for mercy.
The Ur-Quan impounding the Syreen ships instead of scrapping them seems like a major case of fridge logic-until you realize that they might have wanted to pick the Psi-technology apart to figure out how it works and more importantly, how one goes about defeating it. After all, psionic attack likely holds special terror to the Ur-Quan, owing to that race's history.
And the ships being impounded rather than scrapped or analyzed immediately also makes sense; presumably the R&D department saw their budget slashed when the Doctrinal Conflict broke out.
Also, the Kzer-Za may allow conquered peoples to change their minds about being fallow races and become battle thralls instead. We know from the Spathi that they don't allow battle thralls to become fallow races, but they might allow the reverse.
The Druuge treat themselves as things to be exploited, to the point where it's stated (and a part of their gameplay mechanic) that under-performing crew literally get thrown into their ships furnaces to be used as fuel. Now realize that the Druuge's appearance consists of disturbing ape-like arms, a piggish face, eyebrows that look like devilish horns, chains that literally keep them tied to the ship, and finally... a red shirt with a triangle on it. All of the Druuge race are literally red shirts to be used and thrown away. Scary.
The Spathi ship seems curiously powerful for a race of generally comically-portrayed cowards... until you realize that, as a race of cowards, it's completely logical for them to invest as much as possible in really big guns. Hayes even warns about the fact that they're Not So Harmless Villains in his description of them.
Exactly. They're cowardly, not stupid. Well, OK, they're also stupid, but they're at least Genre Savvy.
They're silly, not stupid. Fwiffo/some other Spathi, when you prompt him to give you stuff, gives you some advice: "Don't presume we are stupid." They became an atomic power within a century of their bronze age when given sufficient motivation. Remember, their best guns are rear-mounted. Away from where they're going.