Instructions
Grab the .zip file and use either the BPS (recommended) or IPS patches into a clean EarthBound ROM by using Lunar IPS, FLIPS or Romhacking's Online Patcher. Additionally, the hack can be patched by using DeltaPatcher for the .xdelta patch. EBP patch has been removed in favour of the BPS patch, which should be the one used to avoid glitched/undesired behaviour due to wrong base ROMs.
If you want to use the hack with MSU-1, grab the PCM pack released alongside this hack from the Zeldix page at the beginning of this page, or from the following link: https://archive.org/details/earthbound-msu-1-pack (with a mirror at Zeldix.net: https://www.zeldix.net/t1931-earthbound-msu-1 ).
Simply rename your ROM to "eb_msu1.smc" and place it in the same folder as all the .pcm/.msu files.
You need to use Snes9x v1.54 or above in order for the MSU-1 hack to work.