Miscellaneous items:

Uni-Soulstone
Bob - In a remote forest somewhere

Hand of Creation
Bob - In a remote forest somewhere

Blue Goo
Eidolon - Several Hours Pass...

Odin Materia
Excal - Whatever gets the job done

Manuel of Canuckleheadedness
SYE - Poorly timed Substory

Soulstone
Krono - Early Eidolon 1

Lumberjack GGundam
Excal - Mid Eidolon 2

Scroll of Sound Death
Krono - Hmm...

Orb of Black Fire
SRGPI - A day after Excal/SYE's venture

Black Omen
Krono 

Quantum Stone
Bob

Amulet of Infinity
Krono

Guide to World Domination
Excal 

Chorizite
SRGPI

Moogle Charm
Reako

Genji Glove
Reako

Offering
Reako

Cerberus GF
Excal

Holy Wars
Bob

Small Crystal
SRGPI

Ruby
Eidolon

Artifact #12
SYE

Kupo Nuts
Bob

Chibi SD Daryl 'n Valen action figures with Real Throat-Strangling Action
SYE

Gray's Anatomy
SYE

Rune of Apathy
Excal

Rune of Constipation
Excal

Spekkio's Memoires
SRGPI

Shard of Mediggo
SYE

Immovable object
SYE

Infinija's Mask
Reako

Excal's Mask
Reako

Package
SYE

Zora Masks
Valen

Orb of Lesser Magics
Reako

Mogle Plush Doll
Eidolon X

CopyCat Mask
Reako

Chaos Seal
Eidolon X

Evil Villain's Pocket Guide Vol III
Reako

Crystal of Mid Magic
SRGPI

Sun Stone
Reako

Exploding Crystal with Pain +80
Daryl

Cat Necklace
Bob

High-Magic Crystal
SRGPI

Drake's Mask
Reako

Bard's Mask
Reako

Daryl's Will
Daryl

Enemy Skill Materia
Excal

Life Orb
Valen

Frequent Death Card
Liquid-X

Pendant of the Maiden
SYE

Pearls of Breathing Water
SYE

Oxyale
Excal

Legendary Necklaces
SRGPI