The Exo-Toa Powered Armor robot from BIONICLE is one of the most sought-after and hard to get sets due to its popularity with the fans. But as the head of the Story Team reportedly disliked the toy, he specifically instructed the writers not to give it much of an impact in any media, so the armors were only used by the heroes for half a scene (an admittedly awesome scene) in the comics and novels before they discarded them for blocking their powers, and had only a handful minor cameos afterwards. In fact their biggest contribution to the story was when their destroyed pieces crushed a villain.
The Skopio XV-1, an impressive transforming Spider Tank, the king-piece of BIONICLE's 2009 line, and also its largest (piecewise) and most expensive (at the time of release) set ever, only appeared in a short side-story released in a Polish magazine, in which it got promptly trashed by the heroes and was never used again. Granted, the Skopio beast, which the XV-1 tank has been modeled after according to the story, had a memorable appearance in one of the Direct-to-DVD movies, and it was even animated to look almost exactly like the Skopio set (which, again, represented an artificial Skopio, not the actual animal), however it also lasted for only a single scene.
Takanuva's flying Cool Bike, the Ussanui, is only in the story for a few seconds 'till he crashes it.
Magic the Gathering's expansion Guildpact featured, on a single card, Fblthp, a little lost Homunculous. The card, Totally Lost, is not usable for competative play, but is still fondly remembered. He eventually became popular enough to warrant a plushie!