I believe all single game HES releases has the manual printed in the inside of the box inlay (front), well except for Pyramid which included an AVE manual.
All HES exclusive (and not so exclusive) multigame carts... the 6pak, total funpak, mindblowerpak and funblasterpak includes a "paper maual", the two Maxi15 revisions includes the AVE manual though.
Cardboard box releases mostly included a copy of the inlay from the VHS type cases? at least that's what most of mine does.
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N64 Wanted List:
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Clayfighters 63 1/3: Sculptor's Cut (I)
StarCraft 64 (CIB) - PAL
Worms Armageddon (CIB) - NTSC
Legend of Zelda: Majora's Mask (Grey NFR Cart)