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.
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.
First, it's probably up to your DM. Since Prestidigitation can't duplicate the effects of a higher-level spell, and the text of Diguise Self reads, in part:
Your DM might rule that Disguise Self, at the most minor end of its range of effects, covers the effect of changing skin colour, therefore making that use of Prestidigitation disallowed.
Apart from that possibility, colouring skin certainly seems within the range of what the spell could accomplish by its description. A face fits within a 1-foot cube, and three separate foot-cubes (for 3 rounds, or 18 seconds) could cover face, hands, and feet.
To colour all skin, you'd have to focus on a section of body that fits within a 1-foot cube per round. Very roughly, a 6-foot tall human body has two arms 3 feet in length, two legs of 3 feet in length, a head that fits within a foot cubed, and a torso that's about 3 feet tall and slightly less that two wide, but with hips and shoulders already included in the approximate measurements of the limbs:
That gives (very roughly) 15 foot-cube sections of body. So to colour the whole skin would take 15 rounds or 1-½ minutes.
However, human skin is in reality very diversely coloured even on the same person, so such a disguise would look odd under only cursory inspection—they'd have perfectly flat-coloured skin everywhere. On the bright side, this flatness might convince a DM that Prestidigitation doesn't duplicate even the most minor use of Disguise Self.