By this I mean one a character makes to sort of reflect on how they have been acting and possibly figure something out? For example: if someone villain has secretly been trying to tempt them into becoming evil and you let the character do a check to see if the realize "Oh (redacted), he's turning me evil". What skill or whatever would be used in that situation?
That or a straight wisdom check, at a lower DC of course.
If someone is trying to temp a character into evil sense motive would be the appropriate skill. This would fall under the Hunch heading. If used this should be done at the time when the temptation occurs. This should only be done in really obvious situations.
If you are talking about reflecting back on a characters action to figure out if they have started to turn evil there is not really any skill for this. In all honesty there really should not be a non-magical game mechanic to allow someone to determine their alignment. This should be a matter or roleplaying not rolling dice.
One look at any alignment thread will show that there is no real agreement on where the dividing line between good and evil is. Only the most extreme actions are free from argument. I think most people can agree that torturing and killing an innocent person for no reason is an evil act, and that saving a innocent baby from harm is a good act. Beyond this arguments start to creep in. Keep in mind that even in the real world most of the people who would be considered evil do not think of themselves as evil. Even some of the worst villains in history thought they were doing the right thing.
Even with magic determining characters alignment is no easy thing. Unless you are an undead, outsider or a cleric or paladin you don’t detect until you are at least 5th level. In the case of clerics and paladins they radiate based on who they serve. A cleric radiates the alignment of his deity regardless of his actual alignment. In the paladins case they only radiate good regardless of the alignment of their deity. This is because a paladin is more a servant of good than that of a deity.
To answer the question of whether evil creatures know they are evil, I would say depends on the creatures. While cultists of a demon lord may be able to convince themselves what they do is somehow a noble goal, I doubt said demon lord is under any such misconceptions. On that note, if a creature is evil but thinks they're good is would there be some check for them to realize they are evil? Not to say that would necessarily mean they would have a change of heart.
I think the real question here is are you trying to inform a player or a character that they are becoming evil?
In general, it is assumed that a player has a) perfect knowledge of the morality of their characters actions and b) complete control over their characters moral actions.
The first point often fails because a player and gm may have different views on the morality of certain things. When that happens, a good GM will realize it and communicate to fix the error.
If an NPC is doing anything to with lying or manipulating a PC a character would certainly get a sense motive check to know that. Typically though, if a NPC tells a character something like 'it is ok to murder that person because he is a halfling' then the player won't be in any doubt that murder is bad, but they may choose to play their character as being easily led to the dark side, or, if they choose, even if the character is convinced by the NPC that murder of a halfling isn't evil, they could generally still have their character refrain from doing such a thing.
The point though is that an NPC might be able to convince a Character that wrong is right, but they shouldn't be able to convince a player. If you a GM think that you may have done so (your NPC argued so convincing for a certain behavior that your players now believe that you as the GM believe that that behavior is moral) then you need to correct the players misunderstanding.
Since we are talking people here, shouldn't it be an apposed check, since a common trait among the less than honorable is a facility for lying to themselves, man is a rationalizing animal after all.
Maybe a wisdom versus charisma check? This would tend to make the charismatic types more vulnerable to self delusion and associated bad behavior. Do you hear that, it's the sound of falling Paladins. ^_^