If someone uses sense motive on someone who isn't trying to lie (and thus wouldn't be making a bluff check), how do you decide the DC (since you're not doing an opposed roll in this case.)
Well, usually if you tried to lie you would have the player roll a sense motive in response, they wouldn't just roll one for no reason.
If a player initiates a sense motive, they are probably trying to use the 'hunch' aspect of the skill to get a basic feeling about the other person, which is a DC 20. That would let them know if the person was trustworthy or something similar, but wouldn't particularly tell you anything about a specific statement, other than that they have no reason to suspect it being deception.
In these cases you can treat these rolls as "getting a hunch":
Hunch: This use of the skill involves making a gut assessment of the social situation. You can get the feeling from another’s behavior that something is wrong, such as when you’re talking to an impostor. Alternatively, you can get the feeling that someone is trustworthy.
By default it is DC 20 roll. If they succeed you can tell them "They seem genuine." and if thet fail you can say something like "You cannot tell whether they are genuine or just good at lying.", which would also be a standard response if they fail against Bluff.
That depends. What is the character trying to accomplish using Sense Motive? If the target isn't lying, then there's nothing to perceive, so there is no DC--any Sense Motive roll is just a charade.
If you're doing a "hunch" check to assess the social situation around the speaker, the usual DC 20 check should provide positive assurance that the character is trustworthy. That takes longer than just hearing a sentence, though--it can take anywhere from a minute's worth of conversation to hours of observation.
Edit: Houserule-wise, I sort of combine the two for fake Bluff checks--a Sense Motive roll of 20 gives "You think that they believe what they're saying", while less than 20 gives "You can't be certain". I generally don't do the "You think they're lying" when the subject is telling the truth as it tends to create more problems than it solves. Pathfinder just doesn't model that situation very well.
I meant for times when someone is telling the truth but the PCs have a good reason to think they are lying
Whenever someone makes a Sense Motive check, you should always roll a d20 behind the screen so they don't know whether a check is being made or not.
You tell them the NPC appears to be truthful if:
Truth 1: NPC is not attempting to deceive AND your flat check was low (say, 1-18).
Truth 2: NPC is attempting to deceive AND their Sense Motive was low.
You tell them the NPC appears to be lying if:
Lie 1: NPC is not attempting to deceive AND your flat check was high (e.g. 19-20).
Lie 2: NPC is attempting to deceive AND their Sense Motive was high.
This way, there is a chance they think the NPC is lying even if the NPC is not, which is important in long-term scenarios.
It's a hard one because many people can't tell the difference between the GM witholding something and the GM playing a character who is witholding something.
I have a little Excel script on a laptop to make the die rolls when I require them. Amongst other uses I roll it every time I play a character bluffing the players and tell them that they think they are being bluffed if the roll is successful.
The players are aware of my solution and can trust that I always tell the truth as their characters perceive it