Takua in BIONICLE started out as the Featureless Protagonist of a little-known Game Boy Advance game. After he was again the main character in a very successful online game (moving from AFGNCAAP to having his own identity only at the very end), his popularity exploded. In 2003, he was the star of his own Direct-to-Video movie where he became Toa Takanuva and was released as a toy set twice (once as Takua and once as Takanuva). Then he and the other 2002-2003 characters returned in 2008 (complete with new toy figures), with Takanuva being the star of the first Level 3 Readers book and having an online blog that narrated the events of the final (regular) book. And his was the largest figure. He was released again as a Stars commemorative set in 2010.
Also of note are the Toa Inika. When the story moved to a brand new location (Voya Nui) in 2006, LEGO decided that, rather than create six new Toa characters, they would just take probably the six most popular Matoran characters (Jaller, Hahli, Hewkii, Kongu, Matoro and Nuparu) and turn them into Toa, via space lightning.
Equally significant is the 7thPirakaVezon, a character who was an accidental clone of one of the other Piraka. He was the 2006-2007 Big Bad, but was just so wacky that fans loved every appearance of his, whether he was drafted to free an offscreen former Big Bad who defected pre-series, or simply went on madcap interdimensional adventures.
A very minor on-line game character, called Tiribomba, developed a small following, despite having done absolutely nothing to contribute to the plot. The reason for his popularity lies in his wicked awesome name.
The Alley Viper figure from the original G.I. Joe line has a huge cult following amongst GI Joe fans, to such an extent that it was quickly re-released within two years of its initial run in circulation.
Same with the Crimson Guard figures; this was most notable during the GI Joe Vs Cobra/Valor Vs Venom years, when Hasbro built a new Crimson Guard mold and opted to not release as part of the regular series, opting to make the figure a Toys 'R Us exclusive. To ease fan anger, the figure was largely released in a series of army builder sets, meaning fans buying the figure could build their own units without having to buy multiple figures.
Mimic, a garish green unicorn from the 1980s My Little Pony line, reportedly did poorly in sales in its initial run. On today's second-hand market, prices soar.
It's been speculated, though, that Mimic's poor initial sales are what made her so hard to come by, and are the reason for her value today.
Firefly may be the queen of this trope. From the moment she was introduced, she was arguably the most popular of all the ponies. Even though she wasn't in much of the series, she was depicted on a ton of merchandise. When Rescue from Midnight Castle was rereleased on video in the 1990s, it was renamed Firefly's Adventure, even though Megan is really the main character. Lauren Faust even based Rainbow Dash's personality on her. (She would actually be Firefly if not for copyright issues).