For spells, Power Word Stun does not allow the player to make a save. This should be a long enough stun to allow the NPC to tie up the PC or knock them unconscious.
If the player does not have trap sense, you can always use a trap to apply some sort of sleep affect. Fuss is usually created when the player feels his characters life is at risk, so if you do not have an enemy present, and instead it is just a form of sleeping gas, the player is more likely to be okay with it.
For these sort of scenarios, I would keep it strictly role playing. "You feel a blunt object smack against the back of your head for a split second, before the lights go out...". Out of game: "Okay, your character has just been knocked un-concious, don't worry, no harm has come to your character, this is an event that triggers in the story line when the party gets split up. For the next couple of scenarios you will assume the role of a doppleganger with this goal in mind..."
From there you can add in your own twist depending on how the player reacts. Say for example, the player does not like the idea of back stabbing their own teammates. Tell them that off on the side they will have the ability to attempt to escape, and potentially make it back to the party to warn them just in time. The ways in which you can avoid conflict between 'fair' and 'unfair' scenarios is endless based on how you word things!
Also, saying they got shot by 20 darts, and have to make 20 fortitude saves to avoid being put to sleep is a bad idea. Why? Because you are trying to justify an inevitable situation with an in-game rule. You give the player a glimmer of hope and waste their time in saves just to take it away from them anyway.
I had a scenario similar to this where our group ran into a Naga caster. It had already felt like the DM was out to kill a specific party member, and sure enough when the Naga used mass charm the only person to save was that targeted party member. The DM then continued to spam sleep spells until that solo character eventually failed. He then had the charmed PC's go to the Naga's house while the Naga said "I'll be right back, please wait here" and then performed a coup-de-grace on our party member. As players we were not allowed to attend to our sleeping friend because "that was meta gaming" and "you see the naga as friendly, you have no reason not to listen to her request" thus we could not leave her house or avoid going to it in the first place. In the end that solo player succeeded on a total of 6 DC 17 saves, and died because of it and was in fact punished for succeeding the very first one. Moral of the story: Don't give the players saves if something is going to happen to them inevitably, that is a dick move (Also don't make killing them inevitable).