There have been several questions about how the credit system works, so it would probably be good to have something about it in the OP. Here's the gist of it:
"Credits" are a type of currency introduced in Metroid Prime 3: Corruption. Think of them like Xbox Achievements, but they can be used to buy cool things from the extras menu, like a screenshot tool (used with up on the dpad), or a bobblehead of your Mii in the ship among other things.
The system was brought into Metroid Prime Trilogy, where you can do things like use the Fusion Suit in Prime and see concept art of all the games. Since Prime 3 was built with this mechanic in mind, it has a
ton of credits to go out and get. The other games had this feature ported in, so they do not have nearly as much. Here's what they are:
Metroid Prime
Orange Credit: You get these from beating all of the bosses in the game. Since you will face all of the bosses as you play through, you will automatically get all of these once you beat the game.
Silver Credit: You get these by accomplishing some objectives, such as beating the tutorial and getting all of the Artifacts (required to beat the game). However, two of these are only acquired when you fill up 50% and 100% of the logbook, so you need to get all of the scans to get all of the silver credits. There's also one for getting 100% of the collectable items, so you'll need that, too.
Metroid Prime 2: Echoes
Purple Credit: You get these from beating all of the bosses in the game. Since you will face all of the bosses as you play through, you will automatically get all of these once you beat the game.
Silver Credit: You get these by collecting all of the 18 Keys in the game (all required to beat the game). Note that you do NOT need to scan everything in Prime 2; that's just a personal achievement if you want to do it. Also note that Silver Credits can be acquired in both Prime 1 and 2, so if you're short one credit, you can get it from the other game.
Metroid Prime 3: Corruption
Gold Credit: You get these from beating all of the bosses in the game. Unlike the other two games, there ARE optional bosses in Prime 3. You will have to beat them all, in Normal or Veteran AND in Hypermode difficulty to get all of the credits. Yes, that means you have to play the game twice to get them all. There are also very tough enemies that appear on each planet once you've beaten its boss, and you'll have to kill each "Red Phaazoid" to get additional Gold Credits.
Red Credit: You get these by scanning every single creature in the game, organic and mechanical. There's actually a glitch in the game where you can get one additional red credit, so make sure to ask if you want to know how to get it, don't want to fill up this post too much!
Blue Credit: You get these by scanning all of the lore in the game. There's also an additional three to get where you have to save three troopers from being killed in the tutorial sequence.
Green Credit: These can only be gotten by having a friend send you Friend Vouchers. As people have said, you can't do this anymore since WFC is permanently down, so
download a save file with 15 friend credits BEFORE playing.
Friend Voucher: Even though these are effectively useless since you can't trade them, you can still get these. Most are little Easter eggs in the game, others are simpler like killing a number of enemies.
Scans
So, to conclude: for MP1, you will need to completely fill the logbook to get all of the credits: that's all creatures, all lore, and all research. For MP2, none of the scans are actually required to get the credits, it's just a fun distraction! And for MP3, you need to get all of the creatures and lore scans. Research is not necessary.
For collectables, only MP1 requires all items for a Silver Credit. But hey, it's nice to see three "100%"'s on the title screen, right...!?
Hope that helps!!!