Spread throughout the game, there are a total of 125 items. This number includes certain items that you get during the campaign (flashlight, guns, etc.) and other optional gear (Fusion Helmet, Hook, etc.). However, the vast majority of these items are pickups that help upgrade your maximum ammo capacity, health, and armor. You can view a more detailed spread of these pickups (including overall %) by pressing select and then LB, while in the game. This will be helpful when trying to figure out what you are missing.
Those of you not familiar with the Metroidvania genre might find its jumbled exploration a bit confusing, but here is a little tip to help clear things up. You need to keep in mind, that you will not be able to access every area at first. You will come across dozens of areas that you will be unable to reach, until you get the necessary equipment required to open them. This might be quite awhile, as there are several key pieces of equipment that you won't receive until much later in the game (Missiles). If you can't figure out how to get a certain item, don't spend forever trying to get it. Chances are, you are missing the specific piece of equipment required to reach it.
You might be a bit overwhelmed at first, when you start to realize how big the map is, and how elaborate the corridors might be. However, this game is a little bit more forgiving, when it comes to finding every little item spread throughout it. Once your character reaches level 20, you will unlock the full map along with the item locations. The items that you have not found, will be marked by a ?. This will be very helpful during the final stretch of the game, when you are trying to hunt down the rest of your items.
Here are a couple things to note when hunting your final items.
The first, is that there are several items located in save rooms. These can be tricky, as your map does not put a ? on that area, because the room is already covered by a save icon. I would recommend making a mental note whenever you notice a destructible door or opening in a save room, that you cannot explore at that time.
Second, is that there are also rooms with multiple pickups in them. The problem with these, is that they will show as cleared (represented by a dot) even when the second item has not been found. I only recall one of these such rooms, but there could be more (see the map for details).
Next, you cannot sequence break to get items if you want the achievement. Sequence breaking is the process of overcoming obstacles in ways not intended by the developers. If you get a certain item (e.g. missles) before you are intended to, that item will glitch and you will not be able to collect all of its pickups.
Finally, I would recommend finding all 100% of the items, before the explosion escape sequence. After this event you will no longer be able to reach the Pulse Rifle, if you don't already have it. It will also make navigation much more difficult, as you will trigger the final boss fight every time you move into the specific area. Although it is true, that you can explore after beating the game, you will still access the final fight every time you enter that area. This will make several areas hard to reach, as a big chunk of the map is inaccessible.
If you are still having trouble, here is a very detailed map. I take no credit for the map, as it was posted on www.Joystiq.com.
Full Map with Detailed Item Locations: