I have one of the non-censored versions of Ocarina of Time. Here's some info:

The Legend of Zelda: Ocarina of Time had the most changes made to it. The original Gerudo Symbol - a crescent moon and star - was changed due to its similarity to the Islamic emblem. The original Fire Temple music was changed because the chanting was apparently sampled from an Islamic prayer.

In addition, Ganondorf's blood was changed from red to green in two of the ending cutscenes to avoid an ESRB rating of T (Teen) and retain its rating of E (Everyone). Unlike the previous alteration, this change is present in N64 "1.2" cartridges. Interestingly, the internal builds in all versions predate the game's release, suggesting that Nintendo intended to release the game with these changes but could not since 1.0 and 1.1 games were already manufactured. Despite that, there is no 1.2 Collector's Edition (gold cartridge), which was the initial shipment.

The design of the Skull Kids in Ocarina of Time featured black skin and pronounced lips reminiscent of 'darkie iconography' or 'Golliwogs' which are regarded as racist caricatures. Other characters of iconic gaming series such as Jynx (Pokémon #124) from the Pokémon series have been accused of being similar uses of derogatory stereotypes. It is worth noting that similar to alterations made to Jynx in the Pokémon series to remove the controversy, the design of the Skull Kid character in Majora's Mask has undergone changes effectively removing potential controversy - in the Japanese version, Skull Kid merely had his prominent lips replaced with a beak (complete with nostrils). In International and GameCube releases, he also has his pitch-black face replaced with a beige-colored head resembling wood, straw or perhaps even fabric. This is in spite of the fact that this Skull Kid is heavily implied to be the same given the Skull Mask in Ocarina of Time. This change is also present in Ocarina of Time 3D.

Edit: I also have a sealed copy of Final Fantasy VII before it hit "Greatest Hits" status.