Bravely Default II partial list of limited-per-playthrough Items (SPOILERS)

Stab & Grab (Knife): Chest in Bernard's Mansion.
Poison Dagger (Knife): Chest in Frosty Forest.
Holy Dagger (Knife): Reward for Side Quest #073: A Message from the Shadows.
Falcon Knife (Knife): Chest in Musa.
Bulwark Blade (Sword): Chest in Underground Reservoir.
Flametongue (Sword): Reward for Side Quest #38: Seek Out That Weakness...Again!
Blood Blade (Sword): Reward for Side Quest #086: To Kill a King.
Catastrophe (Sword): Chest in Fount of Knowledge.
Heavy Axe (Axe): Chest in Miasma Woods.
Big Brush (Axe): Reward for Side Quest #077: A Comic Episode.
Giant Axe (Axe): Chest in Crystals' Resting Place - Wind Room.
Lu Bu's Spear (Spear): Chest in Abandoned Mansion.
Longinus (Spear): Chest in Treetop Tower.
Gae Bulg (Spear): Chest in Holograd Army HQ.
Gungnir (Spear): Drop from Catoblepas (Crystals' Resting Place Boss in Musa).
Yoichi's Bow (Bow): Reward for Side Quest #089: To Arms.
Apollo's Bow (Bow): Reward for Side Quest #078: For the Common Good.
Eurytos' Bow (Bow): Drop from Immortal (Crystals' Resting Place Boss in Musa).
Staff of Life (Rod): Chest in Abandoned Mansion.
Heiji's Jitte (Rod): TWO! Reward for Side Quest #063: Jewellery Heist ; Reward for Side Quest #068: Undead and Unwelcome.
Demon's Rod (Rod): TWO! Reward for Side Quest #066: The Power of Flowers ; Chest in Flying Fortress.
Divine Rod (Rod): TWO! Reward for Side Quest #074: Keep Your Feet on the Ground ; Chest in Chromatite Mines.
Mjollnir (Rod): Chest in Isle of Nothingness.

Gaia Shield (Shield): Chest in Sandswept Ruins.
Moonbeam Shield (Shield): Chest in Waterfall Path.
Bloody Shield (Shield): TWO! Chest in Fount of Knowledge ; Chest in Isle of Nothingness.
Hero's Shield (Shield): TWO! Equip the Bloody Shield in battle 100 times, or equip a Bloody Shield along with another Hero's Shield using Dual Shields.

Lamia's Tiara (Hat): Chest in Serpent's Grotto.
Legion Helm (Hat): Chest in Bernard's Mansion.
Ikaboshi Kabuto (Hat): Reward for Side Quest #046: Test Your Strength.
Giant's Helmet (Hat): Chest in Wrecked Institute.

Floral Robe (Body): Reward for Side Quest #072: A Scary Tale.
Aka-Ito-Odoshi (Body): Chest in Miasma Woods.
Giant's Armour (Body): Reward for Side Quest #071: To Be a King.
Dragonscale Armour (Body): Chest in Flying Fortress.
Genji Armour (Body): Reward for Side Quest #083:  Let Your Light Shine.

Life Ring (Accessory): TWO! Reward for Side Quest #075: The Price of Defeat ; Chest in Crystals' Resting Place - Water Room.
Giant's Gloves (Accessory): Chest in Chest in Crystals' Resting Place - Earth Room.
Mage Shell (Accessory): TWO! Chest in Rimedhal, on the second floor of the first building ; Chest in Jaws of Judgement
Hermes Sandals (Accessory): Drop from Martha.
Black Belt (Accessory): TWO! Chest in Holograd ; Chest in Flying Fortress.
Smiley Badge (Accessory): Chest in Crystals' Resting Place - Water Room.
Wavesong Necklace (Accessory): Reward for Side Quest #081 The Sound of the Sea.
Fairyglow Charm (Accessory): Reward for Side Quest #082: Tree's a Crowd.
Teardrop Brooch (Accessory): In Waterfall Path after the completion of Side Quest #093: Dry Thy Tears. Closer to the southern exit.
Normalizer (Accessory): Reward for Side Quest #091: The Bard and the Beastmaster.