Some sort of automatic patch application. Obviously ips can't be applied to games 256Mb or larger, but it is really high time some sort of autopatching becomes available. With three N64 game editors already released and a few others in development, there will be more call for the feature. You have an especial advantage as well, since you would be the first notable N64 emulator to support the feature and therefore can choose or create the format to be used. In addition, it would allow those who hack ROMs the slight convenience of testing an edit without generating a new ROM image.
(try looking at Ninja. It handles the problem of ips vs rom byteswapping)
Also, a quick checksum check would be helpful, at least as a selectable option. This sort of ties into the autopatching feature above. A warning, then allow the option to run the thing anyway with a proper, masked checksum value. Most S/NES emulators do this already.