The Prestidigitation spell in D&D 3.5 specifically says that it is possible to use it to color items (see SRD). Given the wording, "items" can be interpreted either as "inanimate object" or more generally as "physical entity". It's therefore not clear if the spell can be used to color a person's face (for example, as a joke, or as a rough disguise). The fact that the spell description reports that the saving throw is "see text", but nothing is actually said in the text leaves me even more baffled.
[RPG] Can Prestidigitation color people’s skin
dnd-3.5espells
Best Answer
Prestidigitation is pretty much the catch-all spell for minor magical effects, used to show that magic users aren't limited to just large, flashy spells. The effects listed in the spell description are just examples, and shouldn't be taken as an exhaustive list. It's left vague on purpose, such that players can be creative with their use of magic. The GM must use his discretion to adjudicate the limits of the spell.
I've found that the key behind deciding whether or not an effect is acceptable for prestidigitation is whether or not the the effect would have any serious mechanical repercussions. Anything beyond a minor bonus (+2) to another roll is probably too much. Status effects are definitely not allowed. Also, note this line from the spell description: "Finally, a prestidigitation lacks the power to duplicate any other spell effects." Players shouldn't be allowed to reproduce higher-level effects with such a low-level spell.
That being said, I don't see why colouring someone's face wouldn't be allowed, though if the target is unwilling, you might want to allow for a saving throw. As a rough disguise, it might add +2 to the skill check, at best. Small objects created by the spell look crude and artificial, so I imagine that could extend to disguises created by the spell.