The following can be done after you lock Hollow Bastion.

Blaze Gem: Fat Bandit, Bandit (Agrabah, Cave of Wonders)
Blaze Shard: Red Nocturne (Monstro and possibly other worlds)
Bright Crystal: Defenders (Various places; Traverse Town Hotel has 3 in the hallway)
Bright Gem: Search Ghost (Halloween town and other worlds as well)
Bright Shard: Green Requiem (Deep jungle)
Frost Gem: Sea Neons (Atlantica)
Frost Shard: Blue Rhapsody (Wonderland)
Gale: Angel Star, Invisible (End of the world; screen before final rest save point)
Lucid Crystal: Dark Ball (Various worlds )
Lucid Gem: Gargoyle, Wight Knight (Halloween Town)
Lucid Shard: Shadow (Various worlds)
Mysterious Goo: White mushroom(Deep Jungle, in front of tent)
Power Crystal: Wyvern (Various worlds )
Power Gem: Pirate, Air pirate, Battle Ship (Neverland)
Power Shard: Power Wild, Bouncy Wild (Deep Jungle)
Shiny Crystal: Wizard (Various worlds)
Spirit Gem: Air Soldier (Wonderland)
Spirit Shard: Soldier, Large Body (Agrabah)
Thunder Gem: Aqua Tanks, Screwdrivers (Atlantica)
Thunder Shard: Yellow Opera (Wonderland)
Black/Blue Fungus (Various worlds)