The official Animated DC Universe ends with "The Zeta Project", but "Teen Titans" taking place after it is a decent continuity.
The four following "Batman" movies are a build-up to the "75th Batman Anniversary" movie with the same characters and voice actors of previous "Batmen" but are all stand-alone.
"Young Justice" would most likely take place prior to or during "Justice League [Unlimited]" as the story revolves around 'sidekicks' just as superheroes are becoming popular but inputting it in there in the already existing Animated DC Universe would break-up the timeline. Additionally, it takes place on a different earth in a different timeline/universe, so it can be thought of as a stand-alone. The same can be said of "Justice League Action" as it's a remake of "Justice League". "JLA: Trapped In Time", I'm assuming, would take place as a stand-alone or after "Justice League Action".
The following 22 movies/shorts/series are all stand-alone and sprinkled in to build on the lore of previous characters and their team-ups.
Finally, "Justice League: The Flashpoint Paradox" marks the end of the previous Animated DC Universe jump-starting the canon DCAU based on "The New 52". Saving these for last would make a good conclusion to the stories and lore of the previous movies' characters and "Justice Leagues", and even to all the stand-alones, to start anew in the DC Animated Universe.