Only outsiders may have alignment subtype. So "evil creatures" (mentionned by the spell, aura strength HD/5) who are not evil outsiders (HD) nor evil clerics (HD) nor evil elementals (HD/2) are necessarily evil creature without alignment subtype. Like, an evil human or elf or kobold.
Kyramus, the answer to your question (are kobold babies evil ?) lie in the introduction of the MM. It explains the various categories of alignment frequency. "Always" means the alignment is inherent. From birth, to death. Unchangeable. Exceptions are the stuff of legends, maybe one in a million are possible. All other frequencies are cultural matters. Kobolds are usually evil because they are raised to be evil. This means that kobold babies, their education not finished, are probably still neutrals; and that even if they are already evil, they can be redeemed and taught another way.
As for paladins randomly detecting evil and smiting everyone who "bips on the radar", that's an example of utterly poor roleplay, and the best way for the paladin to be stripped of his paladinhood (remember the thing about respect for life, tolerance, redemption and mercy ? If someone is wicked inside but not considered guilty of anything, the paladin should try to make that NPC amend himself, or at least discover why he's tainted by evil before hitting him on the head while shouting "in the name of justice, I smite thee because you're nasty !").
Usually, being evil is not a crime; it is performing evil acts that is (usually). Now, since alignment is how you behave, someone who's evil probably has made something for that. But the paladin should at least discover what, and get the criminal to repent, rather than bluntly attack on sight without any valid accusation.
And for all dilemna based on unjust laws and paladins... A paladin must serve a lawful good Ideal of Justice -- that is not the same thing at all to human (or dwarf, or orc...) institutionnal justice. If a law say that visitors must sacrifice a baby to Zgubuluth the Dark One before they can enter the city of Zgubuluthopolis, a paladin would never consider this law to be a just and valid law. Furthermore, the militians asking him to comply would be evil (they couldn't be something else and enforce such a vile (and stupid) law); and the paladin's code expressely interdict him to associate with evil people. Obeying evil guards is associating with them, in a way. And it is unlikely a paladin would enter in such a city for something else than cleansing it, so he wouldn't have a law-abiding behavior at all.
Remember, the lawful alignment is a metaphysical notion. That's not a barrister's work. That's not obeying laws. Furthermore, disobeying laws is a duty each time the laws are unjust. If a paladin don't understand that, he's not lawful good; he's lawful stoopid. A last note on this topic, I don't understand why people always seems to believe the lawful tenet of a paladin's alignment is more important to him than the good one. Ultra-lawful behavior is a trap set by devils to turn paladins into blackguard, that's the first, second, third, fifth, seventh, eighth, etc. until last lesson teach in each paladin academy... Oh well. My paladin always see alignment switch to NG as an honorable and wise retirement; but switch to LN as a proof of short-sightedness and an excuse to intolerance. They also have a much easier time to atone if they have stayed good than if they don't. But maybe that's just me.
So, I don't buy the "gestapo" scenarii (number 3 and 4).
About scenario 1: That's a valid one. However, the party was wrong, kobolds are not inherently evil, they're just culturally predisposed to evilness. If there was a paladin in that party, he would have receive a reminder about mercy, redemption, and tolerance from his deity, were I the DM.
Scenario 5: I have trouble picturing good-aligned citizen worshipping something evil. Alignment is what you do, if they have evil practice, they are evil. However, in such a case, I think the only good behavior is to slay the beast, or at least convince the villagers of the wickedness of this cult. For a trully good party, it should not matter if the sacrifice is an elf or goblin.
Scenario 6: In a world where orcs can go to a human village in order to put a complaint to the human sheriff, it's a bit unlikely PCs who knew where they are attack orcs on sight. So, either the orcs have attacked them first (and it's a case of legal self-defense), or the PCs are total strangers, ignoring of the laws, customs, and policies of the place -- unlikely the kind of guy that are given a police's job to do. However, rather than a formal complaint, the orcs may instead ask for reparations, arguing that they were not hostile and that the humans have broken the truce. The dilemna for the PCs would then be: should they go to the orcs and plead guilty to save the village from reprisal, or just let the villager face the consequence of their own acts, maybe helping them fend off the orcs ?
Scenario 7: A baby tarrasque ? Depending on the level, PCs should either try to kill it or flee to another continent. A baby giant ? Capture would be morally preferable, followed by an investigation to discover why the giant mother let her kid wander alone.
Scenario 8 (River 4): Killing villagers to save them would be self-defeating.
Scenario 9 (River 5): Where's the difference, actually ?
Scenario 10 (River 6): Usually, players don't infiltrate these kind of network. They kill or capture and seek documents...
Scenario 11 (River 7): Good players could help the woman escape and hide her, but would definitely insist on knowing a bit more on what's going on. If the evil woman is not found guilty of anything, just of having birthed a freak, they should help her move to another region (if the baby's not evil, it's not an half-fiend baby, just a freak -- half-fiends are always evil, see the MM). If she has committed crime, adequate justice should be done (adequate don't necessarily means "burn her at the stake").
Scenario 12 (River 8): I rather expect players will try to slay the generals...
Scenario 13 (River 9): That disease don't seems that bad, if it just induce wanderlust... What do you mean by "creature of the far realms" ? If they became mindless babbling multitentacled monstruosities with a non-euclidian shape, whispering secrets so perverse everyone around is compelled to enter a blood orgy, they should slay them. If they stay something normal, where's the problem ?
Scenario 14 (River 10): From start. Destroying all life is not a way to be free. Resistance would be the way to go, big centralised, slave-based empire are very vulnerable to guerilla tactics and civil insurrections.
Scenario 17: Were I the rogue's player, I would try to frees the slave and disappear in the shadow. I would give a false identity if some captive would want to know me to thank me afterward. And in fact, I would even encourage the freed captive to loot the noble house as a "reparation", so that my own burglary could pass unseen. Investigation would reveal that the slaves have escaped themselves and then pillaged the house as an act of revenge (and a way to have something to pay new clothing and a night at the inns). In other words, I would use them as a digression if possible.
Scenario 18: Pregnant or just bloated-fat ? In the fury of the combat... If they meet her in a non-conflicting situation ('cause, pregnant or not, if you're attacked by a woman raining fingers of death and other attack spells on you, you fight; and after a real fight it's more than probable there would be an accidental aborption as a result), they should capture her, strip her of her spellbooks and components, enquire a bit about the father, and bring her to justice at the town.
Scenario 19: Why attempting to kill her ? The PCs should rather try to discover if she has indeed the healing powers she claim to have, demonstrate the fallacy of her illusion ("see, that guy who got his left arm torn apart by a boar charge... He seems to have a left arm anew, but he can't use it, and your own hand would pass through it if you try to touch it...") and then see how the villager react.
Scenario 1bis (Ghostwind's): That's the same as the first, the kobold one (except with drows).
Scenario 1ter (ArcOfCorinth's "19"): That's an improvment on the first one. However, the prisonner could probably be brought to the surface, and judged by people having suffered from drow incursions (surface elves, dwarves, anything...) as a prisoner of war (there's a perpetual war, right ?) and judged for the crime of his race (that's not something very in accordance with XXth century western ideals of justice, but that's what you can expect in a typical fantasy world).
Scenario 20: The best thing to do would be looking for a cure to that curse, and hoping they could find it before the next transformation. Alternatively, they could get the villagers preemptively imprisonned in individual cells before they get changed in werebeast, and release them once the transformation is over (or at least, once the cure is found). That would require convincing someone of power to lend a prison for that, and convincing the villagers of accepting that emprisonment (something that's probably possible, unless they're completely rotten).
Scenario 21: Hehe... I understand what your PCs have done, especially if they can't imagine obtaining a fair trial. This depend on the political power of the archnemesis, but if he made this move, he's probably influent enough to avoid a situation where the PCs would turn the trial into a trial against him for label !
Scenario 22: Gah ? That ain't classic D&D trolls, that's sure.
Scenario 23: Quite nice as a dilemna... Myself, I'm rather the kind of people who will explain that it's a king's duty to sacrifice himself to his country..
Scenario 24: The PCs should simply explain their found to the barbarian chieftain. That's not a dilemna for the PC, but for him.
Scenario 25: Not a real dilemna again. What should the wizard do, except getting a restoration spell to get rid of the negative level ? Maybe warning several people (like concurrents of that man, some good churches official, and maybe the duke) that they have reasons to suspect the man is not really reliable.
Some dilemnas of my own:
The PCs are travelling with an evil artifact they need to destroy (a basic divine quest-type adventure).
As they are on their road, they see a kobold running, chased by a pack of gnolls. First dilemna, do they act ? They did. They stopped the gnolls. One of them called reinforcement, however, and an ogremage and some other troops came (including a boosted bugbears and plain ogres). Some PCs were captured, and the evil artifact fall in the ogremage's hand. Now, the second dilemna was about talking. The ogremage guessed that the artifact was dangerous, and wanted to know more about it before trying to release it from its chest. He proven much civil (that is, he didn't intended on torturing the captured PCs), and made clear that he simply wanted answers in reparation for his slain gnolls and escaped kobold slave. The artifact in question is an elfbane intelligent weapon with an overwhelming ego, able to dominate nearly every wielder into going into its genocidal quest. The ogremage sure would not have wanted to have its ego crushed by that of a mere weapon if he knew the artifact's effect, but was ignorant and very curious about the thing the PCs carried. The dilemna was between "should I give him the answer he want, and become more useful as a dish than as a prisoner, or should I take the risk curiosity will take the better of him and turn him into an anti-elf crusader ?" (both captured PCs were elves, by the way). Actually, they refused to answer. One prisoner faked stupidity and claimed not to be aware of what the other were carrying (obvious lie), the other tried to use magic to escape, failed, and deemed too dangerous and uncooperative, was eaten.
