Much like the Logbook featured in Metroid Prime, the Echoes Logbook allows you the ability to scan and record objects, creatures and environments found throughout the game. Hit Start and select the Logbook to view all the entries you've chronicled so far.
When you encounter new scannable objects, press D-Pad left to break out the Scan Visor (for the Metroid Prime Trilogy version: hold Minus and point to the top of the screen). Hover the center reticule over a glowing object and hold L to scan the object (Z in Metroid Prime Trilogy). Once the scan's complete you'll have that object's entry locked away.
Each object resides in their own special category to help better organise the dozens of entries you'll pick up. You'll also notice visible bars under each category name, these represent how many entries under each category you've scanned so far (you'll also see them represented as percentage numbers when scanning something).
Scanning bosses is always a handy way to pick up hints on how best to deal with them, also make sure you scan any boss creature as you'll only have one chance to do so.
Below you'll find all the scannable objects listed under their respective categories as they appear in-game, and all the locations of where they're found. Use each list as a checklist when searching for remaining entries to scan. Objects marked with a * can only be either scanned once, or in very few numbers, so make sure you don't miss them.
For the original GameCube version of Metroid Prime 2: Once you've successfully scanned 40% of all Logbook scans, you'll unlock the Promotional Gallery which is viewable from the main menu. Scan 60% of all entries to unlock the Character Gallery, 80% to unlock the Creature Gallery and finally scan 100% of entries to open up the Boss Gallery. Finish the game initially to unlock both the Rough Sketch Gallery and Hard mode, then complete the game on Hard mode to unlock the final Storyboard Gallery.
For the Metroid Prime Trilogy version: Starting a new game from a completed save file will retain all your Logbook scans from the previous run.
Special thanks to obishawn and their GameFAQs guide for some limited scan clarifications!
History (GameCube version)
History (Metroid Prime Trilogy version)
Conflict (GameCube version)
Conflict (Metroid Prime Trilogy version)
Note: You must scan all nine pillar locks in the Sky Temple Gateway for your Logbook before unlocking the Sky Temple.