(written from a Production point of view)
Lincoln Enterprises, Inc. (originally known as "Star Trek Enterprises") is a mail-order catalog company started by Majel Barrett Roddenberry and Betty Jo "Bjo" Trimble in 1967. Lincoln Enterprises is still in business and specializes in memorabilia pertaining to Star Trek. Currently, the company is headed by Gene Roddenberry & Majel's son, Eugene Roddenberry Jr., and run through the appropriately-named Roddenberry.com website.
The actual origins of the company and its original merchandise are somewhat shrouded in lore. Bjo Trimble has stated in 2004, "Actually, John & Bjo Trimble set up the original Lincoln Enterprises. Neither Gene nor Majel had any idea how to set up a mail-order business, while the Trimbles have put together several such businesses. At Creation Grand Slam, Eugene Roddenberry acknowledged our efforts with a big hug & thanks. He is very like his father, who also believed in big bear hugs" wbm, having added to Desilu Studios executive Herbert F. Solow that Roddenberry founded the company in order to "...give Majel something to do." (Inside Star Trek: The Real Story, 1997, p. 400) No matter what the original intent of the company was, in the late 1960s, early 1970s, it was very notable for the sale of actual production assets from Star Trek: The Original Series, most notably internal production documentation such as (every draft) episode scripts and the 1967 "Writer's Bible". The sale of the former was very much in direct violation of the rules and regulations of the Writers Guild of America as none of the writers received compensation for their sales initially, though that appeared to have been ironed out in a lump-sum deal with the Guild later on. (Star Trek FAQ, p. 41) But even far more notable was the sale of unused, spliced up clips from the series' original 35mm film trims, such as deleted scenes, outtakes and behind-the-scenes footage, either sold as short clippings, or as framed stills, cut from these clippings, then selling for US$1 dollar apiece.  At the time the future Roddenberry couple spin-doctored their origins to customers as being saved from the dumpster by Gene Roddenberry himself, as it was supposedly common practice to standardly discard unused footage.
However, this was far from the truth, as was divulged decades later. By the time Desilu was taken over by Paramount Pictures in the summer of 1967, Desilu Executive Solow already noticed that the normal print run for Star Trek scripts was increased substantially, far beyond the requirements, needed for production staffers actually working on the production at the time. Not thinking anything of it at the time, Solow's eyes were eventually opened a short time thereafter, when Post-production Editor Don Rode dutifully reported back to him, during the pre-production of the third season of The Original Series. Rode needed previously shot, but unused, alternate USS Enterprise visual effects footage for one of the third season episodes. He went down to the vaults where the studio habitually kept this footage, only to find it cleaned out and to be informed by a security guard that Roddenberry and Barret had only a few days earlier backed up a van and cleared out the fault of all its contents. The security guard was told by Roddenberry that the studio intended to discard the footage as garbage. Knowing and liking Roddenberry for what he was on a personal level and usually turning a blind eye to his notorious antics, a now irate Solow reported the theft to his Desilu/Paramount superiors, for this action actually interfered with the series' production proper. However, and much to Solow's surprise, "everybody pretended not to know what had happened". Rode had to do with stock-footage of the Enterprise. (Inside Star Trek: The Real Story, 1997, pp. 400-401) In Roddenberry's defense, Star Trek's new owner, Paramount, had no interest whatsoever in their new property at the time (see: Paramount Pictures: History with Star Trek), and it is conceivable that Roddenberry was able to do what he did with the implicit (but still illegal, as it was not theirs to give away, but rather the shareholders') consent of one or more of its managers, somewhat explaining their non-committal reactions to Solow's findings. As the company also sold production material stemming from the third season, the Roddenberrys had at least made one return trip to the vaults, but Solow had by then already left the production.
Nevertheless, Gene Roddenberry was crafty enough to at least try to legally hide his footprints. It being a theft, was actually, albeit somewhat circumferentially, conceded by Majel Barrett herself, when she later stated in a 1993, with contradictory half-truths interlaced, interview, "Lincoln has been in existence for probably almost a hundred years. It was originally Lincoln Publishing and it was owned by another gentleman many, many years before. His attorney was Leonard Maislich [sic.]. For some reason or another he gave the incorporation to Leonard. I don’t know how it basically happened, but it really belonged to Leonard Maislich until he gave it to me in the early eighties. It [Lincoln] was merely set up for Gene to handle fan mail for Star Trek." (Strange New Worlds magazine, issue 10, Oct/Nov 1993) No records of a "hundred years" ancient "Lincoln Publishing" are known to exist and the "gentleman" in question was actually Roddenberry himself as Maizlish had been Roddenberry's life-long attorney, representing him legally since long before The Original Series. By transferring title to his attorney (who had somehow managed to antedate the company's establishing date to 6 April 1962 through proxy Mort Kessler, Roddenberry's life-long accountant – hence Barrett's "has been in existence for probably almost a hundred years" remark ), Roddenberry had thrown up a smokescreen if the studio ever decided to pursue the matter legally, which however, they never did. As already implied by Trimble and Barrett themselves, there had actually been another, personal reason as well to proceed in this manner, as it was also meant to hide the Lincoln revenues from Roddenberry's soon-to-be ex-wife Eileen as well. Unsurprisingly, and not entirely unjustified as the original Roddenberry couple was still legally married at the time of the incorporation of Lincoln Enterprises, Eileen found out later, and sued all involved parties for damages, resulting in that Maizlish was actually found guilty of "conspiracy to commit fraud" for his part in the deception, though it assessed no punitive damages against him. Kessler, incidentally, settled out-of-court with Eileen.  It was for these reasons why Lincoln Enterprises was not established as a subsidiary of the Norway Corporation, Roddenberry's official production company through which he had always handled his business and legal affairs, but as a separate entity, and also explaining why the early, short-lived company name "Star Trek Enterprises" was changed to "Lincoln Enterprises". Even staunch Roddenberry supporter Trimble could not refrain herself from calling Roddenberry a "conniver" at one point. 
It has been the sole and primary reason why no contemporary behind-the-scenes footage, most notably the in Star Trek-lore famed "blooper reel", has ever been included in any of the later released home media formats, for the very simple reason that the franchise did not have any, courtesy Roddenberry. It was only in 2006 that any contemporary behind-the-scenes footage, through William Blackburn's privately shot behind-the-scenes footage (and therefore outside the purview of Roddenberry's scavenging hunt), became available to the general public on the remastered home media format releases.
It was not only through illegal means that Roddenberry acquired original production merchandise for his own personal gain; He has proven to be equally adept in begging and/or cajoling his co-workers to give up their work to him. Most notably, much of Art Director Matt Jefferies' early, 1964, Star Trek concept design color art (most famously the original USS Enterprise color art, which was the one producers and executives approved as the final design for the build of the studio model) ended up this way in Roddenberry's possession, to be used/reproduced by him as he saw fit, with Jefferies left out in the cold. 
Under its original, short-lived, name, the company has been responsible for the publication of the very first "official" fanzine, Inside Star Trek, which ran from 1968-1969, while the Original Series was still in production. Strictly speaking, the magazine was yet another illegal endeavor, as it was officially neither endorsed, authorized, nor published under the auspices of the Paramount Publicity Department, the legal owner of the Star Trek brand. However, the studio at the time was not in the slightest interested in their recent Star Trek purchase, and was actually looking for ways to cancel the series. As a result, no commercial or publicity activities on behalf of the series were undertaken by the department, and those that had been, such as the free mail-order distribution of publicity photographs to fans, immediately scrapped upon the acquisition of Desilu by Paramount in 1967, a gap that was gratefully filled by Lincoln Enterprises, against a fee this time of course. The fanzine was canceled after the the series was canceled, having run for twelve issues. However, when efforts were undertaken to revive Star Trek as a new live-action production in the 1970s, the company, now under its new name, relaunched the fanzine in 1976, ceasing publication definitively in 1979, shortly before the release of Star Trek: The Motion Picture, having run for an additional eighteen issues. 
After Star Trek was canceled, Paramount Television wanted to sell Roddenberry all rights and title to the series for US$100,000-$150,000 in 1970, but he, knee-deep steeped in the fallout of his bitter and costly divorce from Eileen, was nowhere near able to raise this amount on his own. It was around that time that Paramount discovered that Roddenberry was selling Star Trek merchandise through Lincoln Enterprises, which was formally an illegal endeavor, as he simply did not own the brand. Yet, both parties struck a deal resembling the prior Writers Guild deal, allowing Roddenberry to continue in return of a percentage of the sales, as Paramount also started to realize that their Star Trek property was not a too bad one to have after all. Not yet having a well oiled Star Trek marketing machine of their own, Lincoln Enterprises suited the studio well in raising the awareness of their increasingly profitable Star Trek brand. It has also explained why Paramount has never sued Lincoln and/or Roddenberry for what was essentially theft of studio property in the 1968-1969 period. (Star Trek: The Next Generation - The Continuing Mission, p. 2; NBC: America's Network, p. 220)
In 1974, Lincoln Enterprises Catalog No. 5 came out, offering scripts, storyboards, and other items related to Star Trek: The Animated Series. Available in that catalog were biographies of the two new crew members, Lieutenants Arex and M'Ress. These two biographies are no longer available from Lincoln Enterprises. However, they can be found as "supplemental biographical info" for each of the two characters at StarTrek.com. The address for Lincoln Enterprises was Lincoln Enterprises, 14710 Arminta St, Van Nuys, CA 91402.
From the mid-1970s onward, Lincoln Enterprises expanded their product range by offering merchandise related to other series such as Kung Fu, Search, and other television projects created by Gene Roddenberry, such as Genesis II, Questor, Earth II and Spectre.
In 1996, Laura Richarz and the Star Trek: Deep Space Nine production staff working on "Trials and Tribble-ations" purchased three sizes of toy tribbles from Lincoln Enterprises to use in the filming of the episode. (The Magic of Tribbles: The Making of Trials and Tribble-ations)
- Lincoln Enterprises at StarTrek.com, the official Star Trek website
- Lincoln Enterprises' "supplemental biographical info" for Arex at StarTrek.com, the official Star Trek website
- Lincoln Enterprises' "supplemental biographical info" for M'Ress at StarTrek.com, the official Star Trek website