Most of the DC animated movies are stand alone, with no plot related connection between them. The only connection is the common background of the comics they come from from. Most of them are retellings of one-shot stories or specific arcs of the comic titles. For example, Justice League: Doom is based on JLA #43-46 (2002), the arc titled Tower of Babel. The amazing Justice League: The Flashpoint Paradox is retelling the entire Flashpoint crossover event from 2011 that set up the New 52 DC comic Universe.

The only ones that I can recall as having an order or continuity are:

• Batman: The Dark Knight Returns Parts 1 and 2
  -The connection between them is small, but they are sequels/a two parter. Part 2 is basically the same as the Batman vs Superman film.

• Batman: Gotham Knight
  -This is a mostly non-canon set of 6 short films, set in-between the Christopher Nolan Batman Begins and The Dark Knight movies.

• Mask of the Phantasm

• Subzero
  -These are canon sequels to Batman: The Animated Series cartoon.

• Mystery of the Batwoman
  -Canon sequel to The New Batman Adventures, both of which are sequels to the Batman: The Animated Series cartoon.

• Return of the Joker
  -Canon sequel to Batman Beyond cartoon.

• The Batman vs. Dracula
  -Canon sequel to The Batman cartoon.

Everything else is listed on Wiki for Batman in Animated Film.

As made clear from your comments, you want to know about all the animated films Batman is in, including team films. Here is my take on it by continuity/release order:

Stand-alone films:

The following films are stand-alone films with Batman in them, and do not share continuity with each other or other films:

• Justice League: The New Frontier
• Batman: Under the Red Hood
• Batman: The Killing Joke
• Batman: Gotham by Gaslight (upcoming)

In DCAU continuity:

DCAU is a large continuity of TV shows and animated film taking place in same universe. Below are the films in this continuity which have Batman in them

• Batman: Mask of the Phantasm
• The Batman Superman Movie: World's Finest
• Batman & Mr. Freeze: SubZero
• Batman Beyond: The Movie
• Batman Beyond: Return of the Joker
• Justice League (Secret Origins)
• Batman: Mystery of the Batwoman
• Justice League - Starcrossed: The Movie
• Batman and Harley Quinn

Superman/Batman continuity:

• Superman/Batman: Public Enemies
• Superman/Batman: Apocalypse

Justice League (JLA) continuity:

• Justice League: Crisis on Two Earths
• Justice League: Doom

Batman: Dark Knight Universe:

• Batman: Year One
• Batman: The Dark Knight Returns Pt. 1
• Batman: The Dark Knight Returns Pt. 2

DC Animated Movie Universe

• Justice League: The Flashpoint Paradox
• Justice League: War
• Son of Batman
• Justice League: Throne of Atlantis
• Batman vs. Robin
• Batman: Bad Blood
• Justice League vs. Teen Titans
• Justice League Dark

Justice League: Gods and Monsters: This universe takes place in an alternate universe and has no connection to any of the other films

• Justice League: Gods and Monsters Chronicles (web series)
• Justice League: Gods and Monsters (Film)

Other universes:

• Batman: Gotham Knight (set in the Nolanverse)

• Batman: Assault on Arkham (set in the Arkhamverse)

A few continuities have non Batman films too, which I have skipped.

Sources (Wikipedia):

DC Universe Animated Original Movies:

Batman in film

DC Animated Movie Universe

DC animated universe