The Super Nintendo Version of the game was slightly altered: For the US release, all the Christian symbols (crosses) were edited out. This version was also released in Europe. Since the replacements for the crosses look pretty similar to the original graphics, it's not really clear whether this is censorship or not. The Game Boy Advance version and all later portings (including the Xbox-"Capcom Classic Collection") should probably also include this censorship. Just as usual, the Japanese version is the only uncensored version you will find.
As far as I noticed it, only the first level was altered. All the other levels should be uncensored, since there's no religious content to be found whatsoever.

Comparison between the Japanese Super Famicon version and the US SNES version.

All Christian crosses in the first level were replaced by another, quite similar-looking symbol in the US version.
Left side: Japanese version; Right side: European/US version