For those who want to find every non-essential item as soon as possible.
First off, this guide will necessarily contain a lot of spoiler information related to the different items that you can pick up in the game and the different areas you visit. However, there are no storyline spoilers within.
The guide provides details about what power-ups you'll need to get various non-essential items, and where to get them. If you must already have an item before you enter a room, then that item will not be listed as a needed item for obtaining the hidden item. So "nothing needed" means that when you first encounter the room you should be able to get the item. I intentionally didn't go into great depth when explaining some of the expansions. Between your different visors and the "humming" sound that power-ups make, you should be able to secure most of the items on the room name alone.
Tallon Overworld
Transport Tunnel B
Missile Expansion: nothing needed (check under the bridge)Root Cave
Missile Expansion: grappling hook needed (x-ray visor is extremely helpful for finding the invisible blocks and the niche in the wall)Frigate Crash Site
Missile Expansion: need gravity suit (in sea cove)Overgrown Cavern
Missile Expansion: nothing needed (reach by taking transport to Tallon Overworld East from Chozo Ruins Reflecting Pool area)Great Tree Chamber
Missile Expansion: nothing needed (x-ray visor is extremely helpful, but the blocks can also be found by shooting beams)Cargo Freight Lift To Deck Gamma
Energy Tank: nothing needed (bust great open with a missile)Biohazard Containment
Missile Expansion: nothing needed (look for Cordite door underwater)Hydro Access Tunnel
Energy Tank: nothing needed (bomb jump your way to the top of the shaft with the bubbles)Arbor Chamber
Missile Expansion: grappling hook needed (x-ray visor is extremely helpful -- accessed from the Root Cave)Life Grove Tunnel
Missile Expansion: nothing needed (move to the top of the circle and drop a power bomb)Landing Site
Missile Expansion: morph ball needed (look for a small cave behind your gunship)Chozo Ruins
Hive Totem
Missile Expansion: beat boss (first pack of missiles)Main Plaza
Missile Expansion: boost ball neededMissile Expansion: grappling hook needed (accessed from Training Chamber)Missile Expansion: super missiles needed (look for a big knot on a tree that can be scanned and fire away)Energy Tank: nothing needed (accessed from the vault)Ruined Nursery
Missile Expansion: bombs needed (solve bomb puzzle)Ruined Gallery
Missile Expansion: bombs needed (bomb into hole)Missile Expansion: missiles needed (break wall)Transport Access North
Energy Tank: nothing neededRuined Shrine
Missile Expansion: boost ball needed (raised platform)Missile Expansion: bombs needed (floor)Vault
Missile Expansion: bombs needed (perform a double bomb jump for the last grating)Ruined Fountain
Missile Expansion: spider ball needed (use fountain for a lift)Gathering Hall
Missile Expansion: space jump needed (bomb the panel at the top of the hall)Watery Hall Access
Missile Expansion: missiles neededWatery Hall
Missile Expansion: gravity suit needed (in the underwater chamber)Burn Dome
Missile Expansion: bombs needed (use your newly obtained bombs on the sandstone wall)Furnace
Energy Tank: bombs needed (take the lower hole -- Furnace is accessed from Energy Core)Missile Expansion: power bombs needed (climb spider ball tracks and bomb the critters)Dynamo
Missile Expansion: missiles needed (Dynamo is accessed from Watery Hall)Missile Expansion: spider ball needed (Dynamo is accessed from Watery Hall)Tower of Light
Wavebuster: lots of missiles needed (fire missiles at the twelve weak points; climb as high as possible to avoid plated puffers)Crossway
Missile Expansion: nothing needed (fire super missile at cordite area, scan, use boost ball to reach the two spider ball tracks)Hall of Elders
Energy Tank: ice beam needed (access middle bomb lock)Training Chamber
Energy Tank: nothing needed (boost ball up to the two slots and roll to the elevator quickly)Magma Pool
Power Bomb Expansion: power bombs and grappling hook needed (bust open the wall at the far end of the chamber)Training Chamber Access
Missile Expansion: nothing needed (look for a hidden pipe behind the red tree leaves)Magmoor Caverns
Storage Cavern
Missile Expansion: nothing needed (Storage Cavern is accessed from Triclops Pit)Triclops Pit
Missile Expansion: space jump needed (fire missiles at central pillar, and space jump from behind the back wall -- or you can use the X-Ray Visor)Transport Tunnel A
Energy Tank: nothing needed (do three successive double bomb jumps)Shore Tunnel
Ice Spreader: power bombs needed (see those cracks in the glass?)Fiery Shores
Missile Expansion: nothing needed (it's on the raised catwalk)Warrior Shrine
Power Bomb Expansion: power bombs needed (Warrior Shrine is accessed from Monitor Station)Magmoor Workstation
Energy Tank: nothing needed (use wave beam to activate lava coolers)Phendrena Drifts
Phendrena Shorelines
Missile Expansion: plasma beam needed (ground level ice block in a corner)Missile Expansion: spider ball needed (break cordite wall with super missiles in front of the temple)Ice Ruins East
Missile Expansion: spider ball needed (the rail is on the rooftops)Missile Expansion: plasma beam needed (ground level ice block near a door)Ice Ruins West
Power Bomb Expansion: plasma beam needed (block of ice on a roof top)Ruined Courtyard
Energy Tank: nothing needed (access secret room from second floor platform)Research Lab Hydra
Missile Expansion: super missiles needed (cordite casing on third floor)Research Lab Aether
Energy Tank: nothing needed (break glass tube on bottom floor)Missile Expansion: nothing needed (traverse the morph ball catwalk between bottom and top floors)Transport Access
Energy Tank: plasma beam needed (melt the ice tunnel)Frost Cave
Missile Expansion: grappling hook needed (grapple up to platforms and fire a missile at the stalactite to break the ice lake)Gravity Chamber
Missile Expansion: grappling hook and plasma beam needed (melt ice then grapple up to the missiles)Quarantine Mine
Missile Expansion: grappling hook needed (access this from the Quarantine Chamber where you fought Phendrena's boss)Security Cave
Power Bomb Expansion: grappling hook needed (access this from Phendrena's edge by the tube at the top)Phazon Mines
Main Quarry
Missile Expansion: nothing needed (activate crane with thermal visor/wave beam and control panel)Security Access A
Missile Expansion: power bombs needed (use your scanner)Mine Security Station
Flamethrower: power bombs and plasma beam needed (bomb grating on top floor and then access red door on bottom floor)Elite Research
Missile Expansion: nothing needed (aim the industrial beam onto the last octet of the top floor and fire)Elite Control Access
Missile Expansion: nothing needed (fire missile at crate on ledge; use thermal visor to see it)Ventilation Shaft
Energy Tank: power bombs needed (turn on air system then get tank behind destroyed grate)Central Dynamo
Power Bomb Expansion (first pack of power bombs -- kill the invisible drone with super missiles)Phazon Processing Center
Missile Expansion: nothing needed (when you come from Level 2, head past the crates and to your right; drop down to the platform on the wall and power bomb it)Processing Center Access
Energy Tank: nothing needed (pick this up after beating the Omega Pirate)Metroid Quarantine A
Missile Expansion: X-Ray Visor needed (when you reach the spider ball tracks, power bomb instead; now walk forward and power bomb again; take these tracks over the gap, and use your X-Ray Visor to see the floating platform)Fungal Hall Access
Missile Expansion: nothing needed (there's an expansion under the large mushroom at the bottom)Fungal Hall B
Missile Expansion: nothing needed (bomb the ground below the mushroom near the exit door)Metroid Quarantine B
Missile Expansion: nothing needed (use a super missile on the round cylinder just past the force field on the right)