A trademark of the company's productions beginning in 1969 was a rotating "Produced by" (and on some shows, "Executive Producers") credit seen in the end credits (and in later productions, the opening sequences) of Filmation programs, a device that was supposedly created to allow them to share equal billing (previously, Scheimer's name was placed above Prescott's), although later Filmation productions credited only Scheimer, in the form of his signature ("Lou Scheimer, Executive Producer"), starting with 1982's Gilligan's Planet.

Many of its shows—particularly the productions of the late 1970s and 1980s—are notable for imparting a simple moral or life-lesson (explained by a key character, in a child-friendly manner) in the epilogue.

Lou Scheimer and Filmation's main director Hal Sutherland met while working at Larry Harmon Pictures on the made-for-TV Bozo and Popeye cartoons. Eventually Larry Harmon closed the studio. SIB Productions, a Japanese firm with U.S. offices in Chicago, approached Scheimer and Sutherland about producing a cartoon called Rod Rocket. The two agreed to take on the work and also took on a project for Family Films, owned by the Lutheran Church Missouri Synod, for ten short animated films based on the life of Christ. The project enabled Scheimer and Sutherland to finance their own small Los Angeles animation studio True Line. Paramount Pictures soon purchased SIB Productions, and True Line's staff increased; including the arrival of former radio disc-jockey Norm Prescott, who became a partner in the firm. He had already been working on the animated feature Pinocchio in Outer Space which was soon released by a Belgian company, and also brought in the Journey Back To Oz project, which would be released over ten years later by Filmation. Both Rod Rocket and the life of Christ series credited "Filmation Associates" with "Production Design" in addition to Scheimer and Sutherland as directors; but True Line was not officially changed into the Filmation Associates corporation until Rod Rocket entered syndication in 1963. (SIB Productions, whose logo bore a resemblance to the original Filmation logo, would soon go on to become "Sib-Tower 12 Productions" and produce the first few of Chuck Jones' Tom & Jerry films for MGM, until becoming MGM Animation/Visual Arts for the remainder of the films).

The new Filmation studio would for the next few years make TV commercials, until approached by CBS executive Fred Silverman to do a Superman cartoon. This premiered in 1966, and was followed by several of the other DC Comics heroes, and then in 1968, the first Archie show. Both series greatly helped Filmation's popularity to increase, into the 1970s, when it really scored big with several of its shows (see below).

As with other producers of Saturday morning cartoons, Filmation was more concerned with quantity rather than quality; however, they did make a number of attempts to rise above the standard animated fare and produce reasonably well-written cartoons. The best-known example of this is their animated adaptation of the Star Trek series, which included scripts contributed by well-known science fiction writers and starred most of the original cast. Other favorably remembered Filmation series included a 16-part animated serial of Flash Gordon (originally intended as a movie for theatrical release but shown in its entirety only thrice on NBC); Fat Albert and the Cosby Kids, an animated educational series created by and starring Bill Cosby; and He-Man and the Masters of the Universe, based on the popular line of Mattel toys. The animated adaptations of the Archie Comics characters were also noteworthy for the pop music produced for it, particularly the song, "Sugar, Sugar", which was a #1 hit single.

In addition, certain episodes of He-Man and Bravestarr, in substance, and often animation, were pioneers in children's animated series of their time and paved the way for broader storytelling. Examples include He-Man's "The Problem with Power" which dealt with He-Man believing he had killed an innocent bystander, "Teela's Quest" which introduced a now famous mythology on The Sorceress being Teela's mother, whom she is heir to the mantle of safeguarding Grayskull, the versed continuity shared between He-Man and She-Ra, among others. Likewise, the scripts for Star Trek, which were often written by the same people who had written for the live-action version of the show, tended to be quite sophisticated, and garnered the franchise's first Emmy award.

Filmation had a reputation for exploiting the technique of limited animation to produce a number of animated series with a distinct look. They made heavy use of rotoscoping in later years (beginning with their Tarzan and Flash Gordon series), and they also re-used the same animated sequences over and over, many times, to the point where the Filmation style was instantly recognizable. Veteran He-Man writer Chris Weber noted this in verse, set to "I've Been Working on the Railroad": "Can't you see the kiddies streaming / home to watch him after school? / Can't you hear my boss a-screaming / 'Use stock footage, fool!'"

This frequent use of stock footage saved production money, but often resulted in sacrifice of continuity. This was countered by cutting from one stock shot to another after only a second or two—long enough to set the scene but before the eye could notice all of the unexplained errors. This became part of Filmation style during a period when most TV and motion picture production tended to run minimum shots of 4 – 5 seconds.

In contrast to the rapid jump cuts during action sequences, another Filmation trademark was the recurring use of long establishing shots in which the camera would pan slowly across a very wide background painting, thus filling up screen time with sequences requiring little or no animation. However, these background paintings were often acclaimed for the high quality of their artwork. Filmation also pioneered other animation technologies, particularly in Flash Gordon, which included backlighting effects for the first time in American animation (they were already in use in Japan), including moire effects to represent energy fields (a technique that was later used in He-Man and later in She-Ra). They also pioneered a unique method of generating 3-D vehicle animation by filming white-outlined black miniatures against black backgrounds using a computerized motion-control camera and high-contrast film, then printing the negatives onto acetate frame-by-frame to create animation cels which were then hand-painted. This produced a dynamic, three-dimensional effect which had never been seen in cel animation before and predated the modern use of 3-D computer animation for vehicles in 2-D animated productions (although it had a distinctive "flicker" to it as some of the painted lines went in and out of visibility as the miniatures moved).

Unlike many American studios, Filmation never relied upon animation studios outside the United States for the bulk of its production; Ghostbusters and Bravestarr both state in the end credits that they were "made entirely in the U.S.A.". Filmation did, however, rely on outsourcing once, when the company created its animated Zorro series. It was animated by Tokyo Movie Shinsha of Japan. The storyboards and graphics however, were made by Filmation themselves. Filmation is also noteworthy for its lavish background paintings under the direction of longtime department head Erv Kaplan such as the purple-colored "night sky" backgrounds used in He-Man and She-Ra.