The spell doesn't specify. Personally I think the way that makes the most sense is that the caster chooses what teleports with them.
cue DM saying "You didn't specify you wanted your Staff to teleport with you". I think the way that makes the most sense is as [MENTION=35019]Croesus[/MENTION] put it above. If the manacles can't move, you escape them. If they can, they travel with you.
Note, Perkins' response is to the OP's second question, not the first one.
I would allow misty step to escape a grapple, manacled to a wall, etc. as those are things you can't misty step with. (You can't take another creature, and the wall manacles are not things that you are holding, like a weapon or staff.) However, if you are manacled, ala handcuffs, then I would have the manacles go with the character, just like his clothes, equipment, etc. do.
Other folks may read the spell differently, but that would be my ruling.
To be fair, I never said chooses aloud. It seems a safe assumption that the caster chooses to bring any possessions they don't specifically say they would like not to take.
cue DM saying "You didn't specify you wanted your Staff to teleport with you".