Why do they need to be captured?
Who is doing the capturing? The story's villains? I think if we had more info, we could offer more tailored suggestions.
If this has to happen for the story to progress, I'd caution you that:
1) The PCs may choose Death over Defeat. I've had this happen.
2) Assume that any "Must happen" event will fail. Do you have a plan if you fail to capture one of the group? What if they all scatter in different directions and you cannot capture any of them? Is the attempt on their lives enough to drive the next event?
Now onto the fun part. Capturing these annoying PCs.
As its been mentioned, sleep is a great way to do it. Unless you have elves or some other race that is immune to magical sleep.
A 6th level monk could just stunning fist / trip / beat them for non-lethal damage.
I had a monster that I used for something like this once. I think it was an ogre that had levels in the PrC Lasher from Sword and Fist. I'll see if I can dig up its stat block in my old notes. Basically it would trip people that tried to flee and anyone that stayed close it grabbed and tossed in a bag of holding. One the plus side, to the PCs they just see an Ogre. An ogre that just so happens to have traded its great club for a whip.
Along the magical route you can always use Charm Person/Monster. Just use something reasonable. "Hey, can you come help me with something...." and just lead the PCs off one at a time. You could also do this with a Satyr if it would make sense in your game.
One of the PCs resembles someone that has committed a heinous crime and the realm has sent out a Justicar to capture him/her!
And I'll just throw this out there. Blasphemy. Now, the spell may just out right kill them now since they're 3rd level. But in a level they'll merely be paralyzed, weakened and dazed. Makes it a perfect opportunity to capture them.
Use a monster that has a fear aura with a really high DC. As the PCs flee from the source of the fear, just have a few more pop up to herd them into the trap. And I wouldn't worry if there's a paladin or something that's immune to fear in the group. When the rest of the party high tails it out of there I doubt s/he will stick around. This would work best if the PCs are somewhere were it's reportedly haunted.
And my last one for now. A pit trap. The PCs fall and can't climb out. Eventually a "helpful" individual comes by to help them get out only to capture them, sell them into slavery, conscript them or whatever you want.