I think it'd be a good idea to add a "Stream" option (for PS3 compatible containers) to the #Transcode# folder in addition to the current options already in there. Test case of how this could be beneficial:
Most of my anime AVI files are incompatible with the PS3, so for convenience I put the AVI extension into the "always transcode following extensions" setting. However, I do have a few AVI files that are completely compatible and can be streamed just fine, but with that setting on I am forced to transcode them. If a "Stream" option was added to the #Transcode# folder (making it more of a #Custom Playback# folder), then I could stream the couple as is while leaving the rest of my AVIs to transcode by default.