These are the ones that had me kicking myself in the ass:
Magmoor MinesIn the huge room where the floor is a grated and underneath are those plated beetles that can only be killed with a power bomb (Choclytes or something). Use your X-Ray Scanner on those rock pillars and you will see it. Use the super missile to blow it up and get it!
Phendrana DriftsGo to the room where you get the gravity suit. Up on the roof should be a grapple hook thingy. Use the grapple beam and swing to this small alcove in the roof. Blow it up first.
In the Phendrana Shorelines, there's a rock pillar near the save room with a ice block alcove behind it. Melt it and there's the missile expansion.
In Ice Ruins East or west, and look around for a spider ball track hidden in the dark behind a wall. Go up it and i theres a missle expansion there too.
In one of the upper parts of a research labs, there is a cordite pillar. You know what to do with it
Also in the reseach labs, there is a rail track that you have to jump up, use morphball and follow to the end to get an expansion.
Phazon MinesIn the room near the Omega Pirate boss, blow up the blue containment cell to find an expansion.
Go out of this area and you'll be in the cavern corridor full of phazon mushrooms, etc. Right underneath the door, use a super power bomb to blow a hole in the floor.
Go to Metroid Quarantine A (the room with the floating platforms you can only see with X-ray scanners). If you go to the rock platform right next to the spiderball track that leads UP to the red door, you'll notice that its quite a dark corner. Use a power bomb to blow up the wall next to the spiderball track, blow up the next wall, and spiderball up to the expansion!
These ones i remember cause they are the ones that frustrated me the most. I now have 100% (finally!!), and I just beat Meta-ridley (i'm doing hard mode), so all i need to do now is beat Prime, and I'm done!
Hope that helped!