A problem that can rise up is casting spells with an alignment descriptor. In 3E, Create Undead has the Evil descriptor. Does a LN player become LE because of repeat casting of Create Undead? If a player creates undead and uses them to help build a levee to prevent a town from being flooded, how is this action to be adjudicated?
It's really up to the DM. Some considerations I might make:
a) Is the character ignorant or misguided? If the character doesn't know the spell is evil and legitimately believes that creating undead serves a good purpose, that would be a strong mitigating factor in how I'd assess the action.
b) If the character does know what he's doing is evil, is he legitimately distraught and repentant about the action and prepared to accept the consequences? If the character believes he is simply being pragmatic, that is to say - if you commit an evil for worthy ends it's ok - this implies a shift from Good to Neutrality. Good and evil aren't being considered ends unto themselves, but tools for achieving something the character wants. The less altruistic the use, the less weal is involved in the use, the faster I'd make this shift.
c) How prolonged is the activity? I'm more interested in doing the same thing on 10 days, than 10 times on one day. I'd treat the later as a single action, since there hasn't been time to learn from or evaluate the action.
In general, I'd try to convey subtly why creating undead was evil if my players tried to do so for some noble and pragmatic reason:
a) If you summon up enough undead to usefully help build a levy, chances are you are eventually going to exceed your ability to command and control that much undead. Ooopps. Now your undead are attacking the villagers you tried to save.
b) If you have fresh bodies on hand, chances are these are the bodies of the relatives of the people you are trying to save. This creates all sorts of emotional awkwardness - ranging from anger at the violation against the person's body, to attempts to relate to the body as if it was still the living person (daddy? hug me daddy!?!?!), to fear and anger (the person in question use to abuse one of the still living persons).
c) You've just increased the amount of latent evil in the world. If you cast detect evil, it will be clear that the 'pollution' as a side effect of your spell will linger and spread over time. Likely it will be diluted and swallowed up among the prevailing miasma, but in the particular case of a PC repeatedly casting an evil spell, because that player is a Destined character (having destiny points) there is a 100% chance universe will take notice. Your levy now becomes a minor nexus of evil. It remembers the event that occurred. Evil spirits move in and haunt the area. Minor curses occur to those that linger there. Bodies buried in the area have a small chance of rising as zombies. Any violence that now occurs there will certainly be recorded at least in the form of phantasms and haunts. Anyone that dies there now has an increased chance of becoming a ghost because the immediate environs in the spirit world are now less welcoming and more confusing and painful to anyone that finds themselves in them; it's easier to get lost and not move on, and of course if you are evil the spirits of the place will welcome you and encourage you to not move on. You now have a mess to clean up similar to if you'd poured toxic chemicals all over the place.
d) It's worth noting that my world uses Fear/Horror/Madness rules, and all undead have a fear aura by default. While a zombie lacks the charisma or HD for a strong fear aura, it's still enough to terrify many commoners which in and of itself could have problems. Some of the weak willed and cowardly could potentially drown themselves trying to avoid contact with the zombies. Add to that circumstantial modifiers (it's the body of a recently hanged rapist) or phobias (fear of dead things), and you have a potential mess.
e) I will try to convey to the character that the private experience of casting the spell repeatedly has left a latent taint in themselves, and (particularly if the character has a high wisdom score) that they are noting a persistent change in their own feelings and emotions. They notice themselves looking at the bodies of the living and at the living themselves as mere objects. They notice a hunger for casting the spell again. They notice suppressing of their positive emotions - less joy in meals, companionship, or things that used to cause them pleasure. They notice conversely stronger feelings of disgust and dislike, and perhaps passing moments where they are no longer distinguishing between the living and the dead and find the living revolting decaying corpses.
f) Exposure to the undead could trigger latent necrophile tendencies in the weak willed or susceptible. That neutral kid who was leaning evil but reluctant or fearing to go down that path, seeing the players do this awesome thing with the undead, might now be provoked into seeking necromantic power. That mildly sociopathic person whose evil lay as dormant potential, as yet unacted on, might become obsessed. I'd probably only go this route if I'd prior created NPC's who might logically act in that manner, but if I had them at hand their evil meters might crank up a notch - and ironically the more the PC's tried to cover up the horror of the thing - the more likely I'd consider this a fair non-metagamey outcome.
Similarly, Summon Monster summons monsters with alignments. Are the creatures just stat bags, or do they carry an alignment taint?
In my game? Yeah, they definitely carry alignment taint and they are definitely not just stat bags. Summoning up evil beings is evil, regardless of the purpose you put them too. Spell or no spell, you can't get a Celestial templated creature to knowingly kill or injure a good and innocent being. If you did manage it, woe be unto you.
Similarly, Poison use is usually defined as evil. I have a goblin alchemist whom I play as NG, but who uses poison. Does that make him evil?
See above description of using evil spells. Personally, I see poison as not being inherently evil and more of a moral grey area. Good people avoid poisons because they encourage treachery, prevent mercy, and have a tendency to accidentally effect people you don't intend them to effect. On the other hand, poisoning a rampaging dragon or a nest of giant ants could be morally justified. Executing a murderer by poisoning him with a fast acting painless toxin rather than by some more painful means as an act of mercy could be morally justified. If killing itself can be morally justified, the means don't matter so much.
There can often be a problem of characters in a civilized area. Many typical adventurer actions are not lawful.
Depends on the group. However, in general, if you play with normal Americans you will not get a lot of well described and well played lawful character concepts. Lawfulness doesn't come easy to most Americans IMO (Mormons and a few other groups being exceptions.) So lawful mindedness can be something that they struggle with, particularly if the DM has a similar anti-authoritarian inclination and tends to have all NPCs in authority be self-serving jerks who exclude and alienate the PCs right from the start.
At that level, the game is more like chess than a role playing game, and alignment considerations are almost entirely absent. That is, the players are trained to not consider alignment for their actions.
If they are so trained, it is the fault of the DM. Players that want to approach the whole game as a tactical combat game are best advised to play a neutral character, since in practice that is what they will do anyway.
