I cant believe that no one even mentioned DS9. That series was vastly superior to TOS and TNG. At least in my opinion. It was a bit darker in theme and had more action scenes than you can shake a stick at, but it still featured some incredible episodes, the best characterization of any ST series and pretty much all the good sci-fi stuff any trek fan would want.
IMO the best Trek movie has to be ST6: The Undiscovered Country. It had diplomacy, combat, prison escapes, a suspense mystery and some very memorable acting from all concerned.