For those who want to be certain that they don't miss any of those one time only scans.
The red entry guide lists, in order, the entries that can only be found at a particular point in the game. Read the first entry and keep an eye out for it. Once you fill it, immediately stop and read the next entry. Unfortunately, Metroid Prime does not allow you to copy save files, so be careful that you do not save the game at any point unless your red entries are completed up to that point.
01) Map hologram: scan this in the Space Pirate's Frigate *before* you get the map. You can do this at any map station in the game, but it's best to remember now since there are only a few others.
02) Fall of Zebes: (Pirate Data) this is in the Biohazard Containment room of the Space Pirate Frigate in the beginning of the game (check your map for room names). If you land on the planet Tallon IV without this Pirate Data, you cannot go back for it.
03) Parasite Queen: Scan the Space Pirate Frigate boss before defeating it or you won't have another chance (it'll make the fight a lot easier as well).
04) Parasite: These swarm the tunnels after the boss, but a few can be found just before fighting the boss as well. Again, if you leave the Space Pirate Frigate without scanning these creatures, you won't get another chance.
05) Hive Mecha and Ram War Wasps: This pair defends the first pack of missiles. You'll have to scan under the water from the edge of the central platform to get the Hive Mecha (scanning the red ports that you fire at does not work). Don't forget to scan the Ram War Wasps and the Hive Mecha during the fight. If you defeat this mini-boss without making these scans, you won't get another chance at them.
06) Missile Blast Shield: As soon as you pick up your first pack of missiles (or just before), you should scan the Missile Blast Shield. There are dozens of other blast shields, but it is possible to destroy them all without scanning any of them.
07) Locked Door: This is technically not a red entry, but it may be difficult to track down later in the game. In the Energy Core Room, you'll see your first locked door in the distance over the green water.
08) Barbed War Wasp and Incinerator Drones: Like the Hive Mecha and Ram War Wasps, this boss fight is your only chance to scan these two creatures. There's no special trick for this duo though. You'll encounter this fight just after the Energy Core Room.
09) Flaagrah and Flaagrah Tentacles: These are both parts of the first major boss in the Chozo Ruins. As with all bosses, this is your only chance to scan the pair. You may die a few times while fighting this boss. Be sure to rescan Flaagrah and its Tentacles each time you restart. The tentacles fill the four bomb tubes at ground level.
10) Stalactite: Their are quite a few stalactites in Phendrena and Magmoor, but it is possible to dislodge all of them without scanning one first. The first stalactite is in the Ice Ruins West portion of Phendrena Drifts. You'll need the space jump to destroy it, but it can be scanned from the ground level.
11) Ice Shriekbat: After you scan that stalactite, you should see a cave to its left. If you have the Space Jump Boots, jump into the cave with your scan visor turned on. Do not step forward or the bunch of Ice Shriekbats will suicide attack you. They are in the distance perched under an overhanging ceiling. Scan them before moving forward because they move very quickly in flight. I'm not sure when they stop appearing here either. It's possible that they never reappear after they are killed (by your bullets or their suicide attack), so be sure and get them when you first see them. If you do not have the Space Jump Boots yet, look upward and toward the Wave Beam door from the entrance area of the Ice Ruins West. You should be able to see the overhanging ceiling from this point for a safer and earlier scan.
12) Ice Parasite: After getting the Space Jump Boots, you'll have to enter the Chozo Ice Temple. This location contains two variety of creature that crawl on the blocks. One is common and can be found all over Phendrena, the other is the rare Ice Parasite. After you get the Wave Beam, this creature vanishes so scan them now.
13) Ice Burrower: These are found in Phendrena. I don't have my copy of Prime (out on loan) at the moment, so I'm not sure whether they are before or after Thardus. Sources tell me that they can be found in a room adjacent to the Phendrena Shores (first major area of Phendrena). So check the doors in this large area (particularly the ones that can only be reached by taking the long way around and up or directly by using the Space Jump boots). They'll be in a small cavern with low ceilings digging through the snow. They look just like ordinary Burrowers (which jump out of the ground and spit rocks at you before diving back under). Get them while you can since they are apparently replaced by Security Drones at some point in the game. Thanks to "Joe" for the heads up.
14) Thardus: This is the boss composed of rocks in Phendrena Drifts. As with all bosses, this is your only chance, and be sure that you rescan it each time you die and restart the fight.
15) Aqua Drone: After you obtain the Gravity Suit and you begin exploring the Space Pirates Frigate underwater, keep an eye out for Aqua Security Drones. They appear just like ordinary security drones, but only on your first run through the Space Pirate Frigate.
16) Elite Pirate: The elite pirates are rather difficult to miss since they are such an intimidating foe. Though you do get to fight about three of them during the game, they do not reappear, so be sure to scan one of them.
17) Phazon Elite: After you get Power Bombs, you can reclaim a Chozo Artifact from this guy near the beginning of the Phazon Mines (though it's a bit out of the way at this point). He looks just like the Omega Pirate (Phazon Mines boss) but he's the size of an ordinary Elite Pirate. This is not a second (or first) chance to get the Omega Pirate boss entry, this is a separate entry.
18) Omega Pirate: This is the Phazon Mines boss. As with all bosses, don't forget to scan him each time you die and restart.
19) Meta Ridley: You're almost done here! Again, don't forget to rescan Ridley each time you fight him.
20) Metroid Prime: The end of your logbook. There's no point in approaching Prime with the intent to scan unless the rest of your logbook is filled. Make sure you get the Lumigek and Fission Metroids, which live in the impact crater after the final save point (though you can scan them and go back to save). During the fight, make sure that you scan BOTH FORMS of Metroid Prime. If you're reading this guide as a spoiler (shame on you), you'll know Prime's second form when you see it, since it looks completely different from his first form.
21) Metroid Prime: Just to be redundant, don't forget to scan Prime's second form.
Special thanks to Kevin Sullivan for pointing out a deficiency in the original version (the Ice Parasite) by learning the hard way.