Star Control/Fridge

Fridge Brilliance

 * 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.
 * 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 in his description of them.

Fridge Logic

 * Everything about the Slylandro probes and their misbehavior in the game makes no sense when you think about it:
 * The supposed "programming" error by the Slylandro. First, setting priority values isn't programming, but rather configuration. Second, there is no reason whatsoever for setting the priorities the way the Slylandro did would cause the outcome that occurred. The exact way the priority values are used is not explained in detail, but in a typical program, such values only help the program to decide what action to take when there is no particular reason to choose one or the other. Setting the priority for replication to maximum should be no different than setting it to 11 (higher than any other priority) unless the code was specifically designed to skip instructions when something has a high priority.
 * The supposed program controlling the probes as described by the Slylandro doesn't make any sense for the probe's intended purpose. If the program described is accurate, then the probe will always select the top-priority target and always perform the action with the highest priority. Since targets are never deselected, the probe is never going to pick a different target after the first one either, unless the target forces itself to stop being the target by going into hyperspace. So in fact, the only reason the probes can function at all is because replication has been set as the highest priority action: it destroys the target, so that means a new target can be selected. With the default settings, the probe would constantly record data about the first object it comes across until it gets blown up by some external force, or constantly harass the first ship it comes across until that ship gets away from or destroys the probe.