Like
@carlinb17 mentioned, there are a few effects that won't behave properly with any other PCB than the one they were designed for.... The Deflector, DMD-2, Hydra, Organ Donor, and VHS were all designed specifically for their EEPROM/PCB combination.
The HAARP algorithms will work in the Arachnid / Pythagoras PCBs but it isn't ideal since neither PCB has the "Direction" switch. (One of the knobs would behave as the Direction switch, which might be a little awkward)
The Leprechaun uses one of the internal effects of the FV-1 and doesn't require an EEPROM at all.
The Daydream, Spatialist, Unison, Radium Springs, and any effect in the
EEPROM Builder can be used in the Arachnid or Pythagoras PCBs interchangeably.
Short version, any of the effects listed in the EEPROM Builder tool can be used in the Arachnid or Pythagoras PCBs, but any others may or may not behave as expected. If you plan to swap EEPROMs go with the Arachnid (8 effects of your choice) or Pythagoras (3 effects of your choice).