Hmm, that's something else I didn't consider. On NTSC the top 8 lines (and bottom 8 I think) are drawn but aren't visable on an NTSC TV. I think FCEUltra has an option to show them in NTSC mode.

The emulators can't autodetect PAL/NTSC, at least not with the iNES format. Unless it does a CRC check on the ROM and it has an internal database.