Than getting almost all the way through a game and then discovering you missed something back at the beginning that you can't go back for.

Me, I neglected to scan the War Wasp dispenser boss in Metroid Prime. Other than that, I've got a complete log book. *debates the merits of seeing how fast he can rip through the game a second time* (No, I don't want to bother trying to get everything during my Hard game run-through. I'll have enough on my hands, thank you.)