Acriz: Well, I say the iOS port that became the PC port for Final Fantasy 5. The game is butt ugly. Nothing looks good in that version. The environment sprites: ugly. The character sprites: ugly. The character art is the original Amano art, but that just doesn't fit with anything ingame.
There is a nice blog article that talks about what went wrong. The article doesn't touch on the gameplay at all, and the graphical differences are just aesthetic.
Actually, I just remembered another bad version of a game: Final Fantasy 4 Advance. It's based off the WonderSwan Color version of the game (which has many of the same issues, although it does have a good soundtrack), and they didn't bother to fix many of the issues, making the game much easier than intended. Furthermore, there's a bug that can freeze the game, and even worse, there's a bug that can result in the deletion of save data. The game was rushed for the holiday season, and it shows.
(Note that this refers to the 1.0 release, which is the one the US got. Europe got the game later, but they got the 1.1 release, which fixes many of the issues with the game, I believe including the save deletion bug. Japan also got that version, but unfortunately the US did not.)
idbeholdME: Anything censored is automatically a bad version of a game.
I disagree.
* In some cases, a censored version can lack triggers that are in the original, allowing people who would be triggered by the original to play the censored version.
* Sometimes, censorship can be funny. For example, Final Fantasy Legend 2's illicit banana trade in the English version is much funnier than the original opium trade (and much better than what we see in the DS version's fan translation).