Hans appeared exactly once on a single card in Magic: The Gathering, and never anywhere else, but the flavor text - "'Ach Hans, run! It's the lhurgoyf!' — Saffi Eriksdotter, last words" - was popular enough that he gotmultiplereferences later on including a short story in the anthology Monsters of Magic (called, naturally, "Ach! Hans, Run!").
Arguably, Norin the Wary similarly qualifies, having been elevated from the voice of cowardice on a handful of cards' flavor text to eventually receiving his own (also cowardly) creature card.
There's also Ib Halfheart, Goblin Tactician and, more famously, Jaya Ballard, Task Mage. Jaya Ballard's card has been known to win "best flavour text" votes on fan sites despite the card not actually having any flavour text (she supplies a solid number of fan favourite flavour text quotes on other cards).
Fblthp. Featured solely in the flavour text and art of a bad common card. People are already calling for him to get his own card - in many cases, a planeswalker (the most powerful beings in the Magic universe).
In the Legend of the Five Rings CCG, Toku was originally an unaligned, free card with no abilities and no use other than being fed to demons. Fans enjoyed the idea of Toku so much that they started the "Toku for Emperor" movement, attempting to influence the game's interactive storyline. As a result, Toku became a major player in the game's storyline, going from a peasant who stole a dead samurai's sword to a real samurai, friend of the Emperor, Captain of the Imperial Guard, founder of a Clan, and (posthumously) a minor deity.
This is lampooned in The Order of the Stick, where Nale's "Linear Guild" includes a Drow whose presence prompts the heroes to question, "Aren't Dark Elves evil?" Nale "explains" that that was before they were a player-character race; "The race now consists of nothing but Chaotic Good rebels struggling to throw off the reputation of their Evil brethren." "I thought you said they were all Chaotic Good?" "Details."
Another surprisingly popular race is kobolds, of all things. Despite their status as first-level Cannon Fodder (though their affinity for traps can make them more dangerous than you'd think), they've gotten a great deal of expansion in various splatbooks, including the 3.5 Edition Races Of The Dragon. One of the more infamous Game Breaker builds for the edition, "Pun-Pun", is a kobold.
It's kind of helped that the kobolds have been the setting's Butt Monkeys for so long that they've pretty much run all the way around on the opposite end of the sympathy scale to become woobies in their own right. Plus, nothing feels more satisfying than bringing down the BBEG with a small, scrawny lizard normally considered a CR of 1/6.
The Tome of Magic Binder class is surprisingly popular considering the other 2/3s of Tome of Magic are the mechanically unplayable Truenamer and the mechanically odd Shadowcaster.
In a similar vein, "Complete Psionic" is widely panned as the worst of the "Completes" line released for 3.5. However, one class in the book (the Ardent) is acclaimed for its balanced play, appealing flavor and unique approach to psionics. The Ardent would eventually be adapted to 4th Edition as a psionic class.
When it was introduced in the late 80s, the Planescape setting brought with it exactly three new player races; the Bariaur — a usually Chaotic Good centaur-like race who were hairy humans from the waist up and large mountain sheep from the waist down, the Githzerai — the benevolent counterpart to the Githyanki, and the Tieflings — the several-generations-later result of crossbreeding between humans and fiends. Tieflings became one of the iconic races of Planescape, getting almost as many official Non Player Characters as humans, were massively popular with the fanbase, and even went on to get "kindred" species, such as the Tanar'rukks and Feyri (the orcish and elvish equivalents of tieflings). This culminated in tieflings being one of the first races to be playable in 4th edition. In comparison, githzerai are obscure and rarely seen, whilst only die-hard fans remember the existence of the bariaur.
4e had its own Ensemble Darkhorse race in the Pixies, who were made into a PC race in Heroes of the Feywild and seem to have become surprisingly popular, likely due to the novelty inherent in them being the only naturally flying/tiny PC race and the comedy inherent in playing a goddamned pixie.
To elaborate, Changeling was one of the limited series NWOD games White Wolf release, only meant to have the main source book and five supplements. From the get go the game was at a disadvantage; not only was it contending with Vampire: The Requiem, which was undisputedly the most popular NWOD game at the time, but it also was the revamped version of Changeling: The Dreaming, one of the least fondly remembered games of the OWOD. Combine that with the fact its subject matter (Fairies) lacked the universal appeal that, say, vampires and werewolves had, and it didn't bode well. However, when it came out sales peaked and the Internet was filled with adoration and acclaim for the game and its setting. Sooon the Changeling fanbase was one of the biggest in the community and rivaled Vampire on fans and players. This huge influx of interest got the series three extra books and several more PDFs added to the line, making it one of the stand out titles of the NWOD.
In a similarly unusual turn of events, a piece of prose from the core rulebook of the New World of Darkness, "Voice of the Angel," has merited a stunning number of references throughout the line, up to and including the finale of a sample story in Saturnine Night and a new covenant in Danse Macabre.
And now there's an entire supplement (The God-Machine Chronicle) dedicated to exploring the possibilities of the concept, as well as a collection of short stories written as a companion piece to the supplement.
This culminates in the concept becoming the foundation of an entire game, courtesy of some set-up from The God-Machine Chronicle - Demon: The Descent.
Kharn the Betrayer of Warhammer 40,000 has been embraced by the fandom, declaring him to be a pretty fun guy to be around and focusing on him to the exclusion of all other Chaos characters. It helps that he has a highly exploitable battle cry: "Blood for the Blood God! Skulls for the Skull Throne!"
The AdeptusMechanicus and their military wing, the Skitarii, enjoy quite a lot of popularity. More than their relatively small role in the grand scheme of things and their few appearances would suggest.
Imperial Commissars have a huge role in the Expanded Universe, to the point where it is practically mandatory that an Imperial Guard novel feature one. This is despite their fairly minor role in-game (usually, an Imperial Guard army will have at most three, and their only power is a slightly boosted statline and a Leadership buff) Interestingly, Commissars are always portrayed as at worst a Jerk with a Heart of Gold (which is partly because the two most prominent commissars in the Expanded Universe are IbramGaunt and CiaphasCain), and never as the trigger-happy, Modern Major General, types the Codex portrays them as, executing Guardsmen for uniform violations or losing their buttons in combat.
Malice/Malal, Chaos God of Screwing Up The Plans Of The Chaos Gods. They (or their followers) have only appeared a handful of times in canon, and Games Workshop may or may not be able to use the character due to copyright issues. But you'd never know that from reading fan material.