I think the following needs to be added to The Bible:
GETTING A 100% ENDING IN METROID PRIME ONLY COUNTS TOWARDS ITEMS. YOU CAN PLAY THE WHOLE GAME WITHOUT SCANNING A SINGLE THING, AND STILL ACHEIVE THE 100% ENDING, SO LONG AS YOU PICK UP EVERY SINGLE POWER-UP ITEM.
Now, if you're trying to get 100% SCANS, here are some troublesome ones you need to get the first time through:
--Hive Mecha - Thing that spits out the bees when you get your first missile
--Barbed War Wasps - Bees that come out when the incenerator drone spits flames at the ceiling
--Flaagrah's tenticle.
--Ice Shreikbats - Phendrana Drifts...need to do it the first time through because later they're replaced by baby shegoths.
--Scans on the space station you don't want to miss...Parasite, Parasite Queen, and one Pirate Log.
--Metroid Prime has 2 log entries, one for each form.
--You CAN NOT scan the invisible drone guarding the super bomb power-up, or the invisible pulse bombus down in the fungal part of the Phazon Mines...but you don't need to in order to get all creature scans.
--Also, if Research scans DO count (I don't think they do), make sure you scan a map station before you use it, because you can't scan one after you use it.