The first anime film was meant to tie up loose ends and make sense of certain events in the first season. Later films in the series were more standalone, though still considered in continuity. Interestingly though, the tenth, eleventh, and twelfth movie feature an overarching storyline involving the three Dragon legendaries of Sinnoh.
It is worthy to note that the first movie was once intended as a Grand Finale in the early production process, indicated by early teasers, but that plot was dropped later because of popularity.
There are now eighteen of them, two of which are actually one for the price of two.
Macross Frontier got two: The False Songstress and The Wings of Goodbye, which is like the Do You Remember Love of the Frontier series. In short, like Do You Remember Love, it's an alternative version of the events during the Frontier anime series, but split in two movies, and the last one kinda solved the love triangle... maybe?
The Revolutionary Girl Utena movie takes the series' already-difficult-to-understand (at least for Westerners) Buddhist allegory, compresses it into two hours, and makes it even more allegorical. The resulting head trip of a film requires advanced knowledge of jungian theory, and knowledge of Gnostic belief to understand at all (but is still plentyentertaining if you don't). (Although, viewing the series first, and learning about its symbolism does make the movie much more understandable, particularly the cars.)
The The Vision of Escaflowne movie radically altered characters and motivations, hitting similar themes in a very different way than the series.
The RahXephon movie made similar radical alterations in the attempt to compress a season's worth of difficult-to-understand story into two hours.
Currently there are 4 Bleach movies released. The first is about a group of rebels trying to destroy Soul Society, the second is about Captain Hitsugaya trying to clear his name, the third is about people forgetting Rukia and Ichigo, and the fourth is about Hell.
The '90sSailor Moon anime had three, one in the second season (Sailor Moon R The Movie), one in the third (Sailor Moon S The Movie), and a final in the fourth (Sailor Moon SuperS The Movie). None have anything to do with their corresponding seasons but seem to take place in just 'somewhere' in them. The S movie is the only one directly based on anything, a standalone manga chapter, The Lover of Princess Kaguya, Naoko Takeuchi wrote purposefully for adaption... there are quite a few plot diversions between them though. Oddly enough, the 1st and Sailor Stars seasons never got movies for them...
The SuperS movie is notable for having a traditional episode style title. Its full title is Sailor Moon SuperS: The Movie: The 9 Sailor Senshi get together! Miracle in the Black Dream Hole! The other two don't have any titles aside from Sailor Moon R/S: The Movie. (Though the English dub tacked some on anyway - Promise of the Rose, Hearts In Ice and Black Dream Hole.)
Two movies also premiered with a short special. R had Make-up! Sailor Senshi, which introduced the Sailor Senshi and SuperS had Ami-chan's First Love (based off the manga chapter of the same name). During the run of the SuperS season, a 45-minute special episode was aired containing 3 shorts: An Elegant Metamorphosis? Crybaby Usagi's Growth Diary" a recap of the first 3 seasons, Haruka and Michiru, Again! The Ghostly Puppet Show", which shows what Uranus and Neptune are doing during SuperS, and ''Chibiusa's Adventure! The Dreaded Vampire Castle" which has the Sailor Senshi fight a vampire and is loosely based on a manga side-story.
It does fit in passably, considering the episodic nature of Cowboy Bebop - a reasonably long amount of time could pass between any two given episodes.
Given that Big Shots is still on, but we see a cameo of Andy as a ronin instead of a cowboy (which happened at the end of the episode he was in) it'd easily take place between episodes 22 and 23.
Word Of God stated that the movie is meant to show us the Bebop crew's last full mission together, before Ed's departure and Spike's death. That places it squarely in between episodes 23 and 24.
Ghost in the Shell: Solid State Society is effectively the show's "Third Gig", although it only occupies one film rather than a whole series. It shows. (Not in a directly bad way, it's just glaringly apparent.) There are also two movies, "The Laughing Man" and "The Individual Eleven", which are basically compilations from the two original season arc episodes. These two films have been criticised for compressing the plots so much that they are hard to follow, and also for the fact that the English dubs were not performed by the actors who dubbed the series.
Though if you go by the related sound stage, it's apparently an actual movie in story...On the other hand, a Sound Stage for the PSP games has the Original Generation characters meet the movie versions of Nanoha and Fate.
Another movie was later released retelling the second season. A third movie has been planned.
Pretty Cure has roughly one movie of this sort per series. (If Hikari hadn't been in the first movie, it would have been exactly one per series.) Like the Sailor Moon movies mentioned above, all of them are disconnected from the parent series' plots but seem to take place somewhere along the way.
Tengen Toppa Gurren Lagann had two movies: Gurren Chapter and Lagann Chapter that were essentially summaries of the original series with new animation put in. Don't let that fool you though. In Gurren-hen the beginning of the movie shows Lord Genome's rise to Spiral Knight and fall to despotic tyrant. Then it's pretty much the same until: Adine, Guame, Cytomander, and the new general: Viral (Yes that Viral, complete with his own Enkidu-daiganzan) all attack the Dai Gurren-dan at once. Simon later snaps out of his wangst after trying to climb Suzaku to save Nia. (Suzaku is at least a mile in the air at this point) The generals then combine their mechs to form the Dai-Gan Doten-Kaizan which falls after a combined attack by the entire Dai Gurren-dan (GIGA DRILL BREAKER! DAI GURREN-DAN SHOOT) Lagann-hen then takes the last episode of the series and raises it to the power of itself after: The ENTIRE Dai Gurren-dan (Only Kittan died, the rest of the Mauve Shirts survived) get their own Tengen Toppa Ganmen. (Even Nia) After Lord Genome converts the Big Band Storm all of the ganmen combine to form SUPER Tengen Toppa Gurren Lagann. From Super Tengen Toppa Gurren-Lagann's drill comes Tengen Toppa's drill. From Tengen Toppa's drill comes Chouginga Gurren-Lagann's drill. From Chouginga's drill comes Arc Gurren-Lagann's drill. And from Arc's drill comes Gurren-Lagann. Viral does a Cannonball Attack. And then Simon and the Anti-Spiral fistfight. Then Simon turns his own blood into a drill and goes straight through the Anti-Spiral.
Slayers has five Non Serial Movies, but only the first is considered The Movie. Drawn to the mysterious resort island of Mipross by dreams planted in her head by the ancient wizard Rowdy Gabriev, Lina and Naga get involved in a battle against a demon named Joyrock that culminates in Lina being sent back in time to kill him before he could slaughter the elves of Mipross, an act that is stated to be directly responsible for the existence of Lina's companion Gourry Gabriev.
The movie version of X1999 was produced when the manga was still beginning. Because of this, many plot elements were over-simplified or cut-out completely, with one of the antagonists (Kakyo Kuzuki, who was yet to be introduced in the manga when the movie was made) being replaced with a new character (Shogo Asagi). The movie sets aside the conflict between the individual Heavenly Dragons and Earth Dragons to focus more on the relationship between the childhood trio of Kamui, Fuma, and Kotori.
The Disappearance of Haruhi Suzumiya, based on the light novel of the same name, was released 2010.
Gintama has a movie adaptation of the fan-favorite Benizakura Arc. Also, in 2013, another movie with an original plot was released, supposedly to act as a 'final episode' for the Gintama anime. Though, considering how many times the staff has trolled the fanbase by claiming the show has been cancelled, there is a certain lack of credibility to this...
Doraemon will have more than 30 movies in a year or two, but since the story doesn't have a real ending nor it has any development, plus what most of what the studio's doing nowaday is to remake em'all for new genaration's kids. All Doraemon movies (except some short movies and spinoffs) are considered not the Non-Serial Movie.
Fate/stay night got a movie based on one of the routes in the game: Unlimited Blade Works. Like all anime adaptation movies, some things were cut, some scenes were changed, and some others possibly enhanced.
Dragon Ball has had 19 movies released theatrically in Japan (4 for Dragon Ball, 15 for Dragon Ball Z). The majority of them do not fit into the series continuity and are usually basic re-imaginings of the series sagas (Movie 7 featured three more androids made by Dr. Gero. Sound familiar?). In addition to these, there were 3 made for TV movies (that do fit into the series continuity), 2 OVAs and 3 live-action adaptations (with only one being more or less official). So far, the only movies considered canon are Battle of Gods and Resurrection 'F'.
Legend of Galactic Heroes has three theatrical movies, namely, My Conquest is the Sea of Stars, Golden Wings and Overture to a New War. Incidentally, the first of those three actually predated the release of the first animated series.
Steins;Gate has Steins;Gate: Burdened Domain of Déjà vu. It takes place a year later, and deals with a much different threat. This time, it's Rintarō Okabe's Reading Steiner ability. His memories of the other world lines are overloading it, causing him to shift out of the Steins;Gate world line. As a result, it's as though he never existed, and no one remembers him, except for Kurisu Makise and Suzuha Amane.