It's not a perfect vacuum out there, there is an interstellar medium. You could create non-negligible drag with a huge sail or magnetic field, like a Bussard Ramjet.
I was looking for this as I have always seen the ramjet as the only feasible possibility for non-magical long-term propulsion. Of course that's if we don't find a way to trick the universe into FTL travel.
Flip the ship around and thrust
You use thrust to decelerate. Same thing you use to accelerate.