This is not an exhaustive list; I need to go through my stuff and find all the other loose/incomplete goodies I have, but here is a sample (there are also some more on my tradelist, so check it):
HAVE:
NES:
Megaman 1 manual only (also have the cart)
Shadowgate manual only (also have the cart)
Ultima Exodus manual only (also have the cart)
some other NES manuals and original posters, will have to check
SNES:
Final Fantasy 2 manual only
some other SNES manuals, maps, a few boxes, posters, will have to check
Genesis:
NBA Jam Tournament Edition box + insert, can't remember if it has the manual will have to check
Technocop manual
some Genesis posters
WANT:
All the good stuff...
NES manuals and boxes, particularly Megaman 2-6, Zelda 2 box + instructions
SNES manuals and boxes, particularly everything for Chrono Trigger and Earthbound, of course!
PS1 manuals and/or boxes, I'll have to make a list
PS2 outer boxes/extras for all the collector's edition Atlus/NIS games like Growlanser Generations, Magna Carta, Stella Deus, SMT DDS 1, SMT Nocturne etc.
Genesis boxes/instructions/maps for Shining Force 1 and 2, Landstalker, and Shining in the Darkness
GBA boxes/instructions/maps etc for Breath of Fire 1 and 2, Shining Force 1 and 2, Mario vs. Donkey Kong, others
Gamecube instructions for Zelda Collector's Edition
Sega Saturn boxes/instructions/maps etc. for Shining Force 3, Albert Odyssey, Shining the Holy Ark, Shining Wisdom