Ascended Fanon: The names Randi, Purim, and Popoie (the Boy, Girl, and Sprite respectively) for the main characters. Square considers these names canon; they're in the guidebooks and default on iOS. Canon Fan Nicknames!
The iOS port romanizes their names as Randi, Primm and Popoi.
Fan Translation: The "Enhanced" version of Secret of Mana uses a much more efficient system of text placement, allowing for a lot of text that was Lost in Translation to be added back in. However, most of the "lost" text was also made up out of whole cloth by the translator. Among other things, the Cannon Travel Service menu now displays the names of the destinations rather than 1, 2, and 3. You can get it here.
Urban Legend of Zelda moments occurred thanks to reviews found to be written by test players who spoiled some things about the game before it was released beyond Beta.
The things mentioned, and later removed due to size constraints, were the Ruby Arment (can be found via cheat codes), Mana-Drops (a mystery item called ??? in English and '...' in Japanese) that could cure all status, heal all health, and recover all magic, a fourth character (one of 4 recruited NPCs that acted as Stand-Ins for a missing character during plot points, later removed but left in place with a cheat code they could be activated), 9th level magic (can be randomly accessed by stat growth of spells when cast in succession which only include extra animation and power), and the fabled 9th element called Life / Mana / Solar which have icons and a stand in slots in the spell ring when accessed by using a cheat code to restore slot-spaces (not available in the normal game despite rumors) but are broken bits that do nothing in the game even with a cheat code.
Lots of people spent hours, if not more, looking for the non-existent Sword Orb that would supposedly give you the level 9 sword upgrade. The cruel irony is that the level 9 sword is actually the reactivated Mana Sword, which you can't get until the final battle.
However, there exists a glitch to get another Sword Orb (basically glitch your party into the start of the game and re-fighting the first boss), which gives you the Level 9 Sword full-time. You can find instructions for it here.
The existence of Level 9 weapon orbs, period, were thought to be a rumor until they were discovered to be extremely rare random drops from enemies in the Mana Fortress.
What Could Have Been: The SNES CD-ROM debacle. By all reports, having to strip this game down is what led to the schism between Square and Nintendo in the latter 90s and drove Square into Sony's arms. To this day fans lament the game we never got, and wonder what could've been had the game come out in its original design (and with Square's loyalty to Nintendo intact)... The very level of the game that we did get indicates how good What Could Have Been was.
Special mention should go to the English script, which suffered the most from the CD-cartridge transfer. Ted Woolsey himself later remarked that the localization "nearly killed" him, mentioning that "about 40% of the text" had to be "nuked" due to space restrictions.