There is a scene in the first episode that contains an animator's inside joke. Hikaru crashes his Valkyrie into a building marked "Studio Nue". This was the name of the animation studio that produced Macross. Studio Nue's mascot, a grinning imp creature, was also on the building. If you watch closely, you can see the imp react in horror as Hikaru careens toward the building.
The companies that designed and built the VF-1 Valkyrie are Stonewell/Bellcom and Shinnakasu Heavy Industries, which is a nod to real world aerospace companies Rockwell and Bell. Most if not all other mecha in the show have the same kind of references for its builders.
The codename for the Macross bridge is Gunsight One. Gunsight One was a Gundam fan club founded by some of the staff members (such as creator Shoji Kawamori and character designer Haruhiko Mikimoto), mecha and anime fanatics on their own right.
The show's production history was a turbulent one: Originally proposed in 1979 after the success fo Gundam, the show was sponsored by a group called the "Wiz" corporation, who were prepared to fund a 48-episode run. However, by 1981, Wiz had gone out of business, and the Macross seemed to be in permanent haitus. Big West, an advertising agency looking to branch out into animation sponsorship, approached Studio Nue about the project, and sponsored it. However, they insisted on a leaner budget, not convinced that the show would pan out as profitable. Big West pared the episode count to 23 episodes (meaning the show would have ended with the battle against Bodolza). Even then, Big West found that the show was going to run more expensive than they had bargained for, and to secure more money, entered into a partnership with Tatsunoko Productions which included international distribution (hence "Robotech" (1985)). When Macross debuted in October, 1982, the stunning success convinced Big West to green light an extension to 36 episodes, allowing the staff to end with the "two years after" story arc.
Studio Nue was unable to carry all of the animation work itself at the time (although the success of Macross meant that they were able to do so with nearly all of their other animation projects),and so work was farmed out to a number of satellite studios, including Artland (Mikimoto's employer), the nascent AIC and GAINAX studios, and the Tatsunoko-supplied AnimeFriend and Star Pro. AnimeFriend and Star Pro are notorious among fans of the show for having brought in very spotty, off-model and continuity error-laden work.
There were plans for a splashy ending to the series, one that would have shown Misa and Hikaru blasting off in the colonization ship Megaroad, but the sequence was scrapped due to lack of time and budget.
The names of the Zentradi spies Warera, Rori, Konda form a complete sentence in Japanese. When rendered into Japanese words, it comes out as "Warera rorikon da". In English, the sentence means "We're pedophiles".
When the AnimEigo DVD release was being prepared for release in the US, there was serious discussion of adding a Zentraedi language track as a bonus. The idea was scrapped.
During the first episode, when Hikaru flashes back to his days with Roy in the flying circus, we can see Roy's old plane. Written just along the seat is the name 'Kawamori' (the show's creator)
Among other production headaches, the master copy of one nearly-completed episode was reportedly accidentally left on a train by a courier, forcing the staff to search for the footage - otherwise they'd have to re-animate it all, at a considerable cost in time and money. They found the reel, and so disaster was averted.