We advocate that master film, which is to be kept in store for long periods, should be wound with the emulsion side outwards. This is because the usual tendency is for film to curl when wound emulsion side in and winding it emulsion side out helps to counteract this.
Note that a study by SMPTE (the Society of Motion Picture and Television Engineers) has shown that films being used for projection in cinemas behave better in projection if they are wound with the emulsion side in. However, for archival purposes this is irrelevant. Masters being preserved should not be subjected to the rigors of projection anyway.