This should go to TCRF at some point... Feel free to make that happen, dear reader.

All

Maps have internal names (e.g. st00_00) that are stored in the ROM but not visible in-game
Do a pass over every ROM with BokMagic and check what shows up
Hidden Tokyo region (default coordinates before selecting a region)
Unused characters in the fonts (e.g. cat in Boktai 1/2, PG## characters in Boktai 3, maybe the corrupted characters from Boktai 1)

Boktai 1

Unused "2" layout for Bloodrust Mansion courtyard
Unused firetop elevator tile map
Unused st02_12 tile map
Unused collision map 0xad33 (muspell) (but check if it's *really* unused)
The two unused chests in Permafrost
Dummied out dark castle sunrise/sunset screen
OoB room in Firetop
Debug strings in the ROM
Debug strings in the scripts ("random num over" or whatever)
The demo ROM is mostly stripped of late game content, but not completely (e.g. the Garmr purification BG is in there)