Do consequences have to show up immediately? I admit it's tough when the PCs can threaten most people with grievous bodily harm and charm anyone who they can't threaten, but if you do to much of that then eventually you become the kind of people that get bounties placed on their heads and other people get hired to hunt down.

Also, people (aka the plot) can inconvenience a party in a dozen little ways if they don't like them (and vice-versa, help them if they are in good standing). Forget to mention that the pass the party is planning to travel through has been shut down by an avalanche. Underestimate the number of orcs in the area. Tell them you're out of stock of healing potions, etc. You just gotta get creative.