Deception is the easiest to handle; PCs get an Insight check opposed by Deception to determine if the target is lying (both rolled in secret by the DM, so players don't know how well they rolled). If the PC wins, the DM announces truthfully whether the target is lying or not. If the PC loses, the DM announces whatever the target wants the PC to believe--usually, but not always, that the target is telling the truth. The player can then act on this information, or ignore it, as he or she wishes.
(If the NPC were the one trying to determine the PC's truthfulness, I'd do the same thing, but apply a modifier to the NPC's Insight based on how plausible the PC's claim is. If the PC wins, the NPC believes the lie. When the PC is the one being lied to, the player's skepticism takes the place of the Insight modifier.)
Intimidate and Persuasion are trickier. I don't usually use those against PCs.
(If the NPC were the one trying to determine the PC's truthfulness, I'd do the same thing, but apply a modifier to the NPC's Insight based on how plausible the PC's claim is. If the PC wins, the NPC believes the lie. When the PC is the one being lied to, the player's skepticism takes the place of the Insight modifier.)
Intimidate and Persuasion are trickier. I don't usually use those against PCs.