Best Treasure Farming Spots
Amber Relic - Found almost anywhere. They are found very common in the Faron Region. You only need 20 of these for all the upgrades. (Eh... meh. Who cares about this thing.)
Ancient Flower - They can only be found in the Lanayru Region. They can only be collected if you trigger the Timeshift Stones. You only need 8 of these for all the upgrades. This includes fixing Scrapper that Lanayru Robot, which only 1 is required. (Pretty flower.)
Bird Feather - The birds can be found only in the Faron Region and you are required using the Bug Net (or the Big Bug Net). You will need to walk carefully towards them and snatch them if you are close enough. The Big Bug Net is highly recommended since it is in fact larger and easy to catch both bugs and birds. You only need 5 of these for all the upgrades. (Boring feathers.)
Blue Bird Feather - Same as the Bird Feather in the Faron Region, but the only thing is that the blue birds are quite rare. If you happen to see one, don't just run after them. Do the same method for the Bird Feather and you'll harvest some Blue Bird Feathers. You only need 5 of these for all the upgrades. (Blue as the sky!)
Dusk Relic - Like Amber Relic, but are in different color. These things can be found almost only in the Silent Realms. So be sure to take a peek at every corner while you are in the Silent Realm. Be sure to pick up many of them as possible. You only need 13 of these for all the upgrades. (Ooh... mysteriously pretty.)
Edit: If you are in the Silent Realm, the best way to harvest as many of them as possible is to get hit by the Guardians and start all over again. You will notice that the Dusk Relics you found will re-appear in the same location. This will reduce your time of harvesting, but you will still need to complete the trail in the Silent Realm. But either way, it's all about patience.
Eldin Ore - Found in the Eldin Region mostly. They are commonly found by digging those digging spots and treasure chests in dungeons. You only need 6 of these for all the upgrades. (These rocks or metals are boring.)
Evil Crystal - These things are hard to come by, but they can be harvested from Cursed Bokoblins in the fourth dungeon. But as long you have the Treasure Medal, it makes harvesting a lot easier. You only need 3 of these for all the upgrades. (They... don't look like crystals to me.)
Edit: If you recall the time where those Cursed Bokoblins were about to get you on the lone rope and there's an escape route above, then that should probably be the best place to harvest those Evil Crystals. They won't die unless you do the Fatal Blow. You can also use your Sacred Shield (or higher) to repel the Cursed Bokoblins.
Goddess Plume - The rarest treasures in the entire game. They can be acquired from treasure chests in the overworld and in dungeons. But really, you don't necessarily need to collect many of them. You only need 3 of them for all the upgrades. (Shiny crystal! :O )
Golden Skull - These things are a rarer version of the Ornamental Skulls. They can be dropped from the Bokoblins, but requires the Treasure Medal for easier harvesting. You only need 4 of them for all the upgrades. (Ooh! Shiny!)
Hornet Larvae - They can only be found in the Faron Region and only from the Hornet's Nests. Just use your Slingshot at the nest and you can pick up the Hornet Larvae. Be careful of those Hornets that may grow furious on you. You only needed 2 of them for all the upgrades. (Seriously? Eww...)
Jelly Blob - These things are really easy to come by. You only needed to defeat any of the Chu Chus for them. You only need 8 of them for all the upgrades. (I like to poke them.)
Edit: In the Sand Ship, which is the 5th dungeon of the game, if you leave the ship into the present (not hitting the Timeshift Stone), then you should see a lot of Arachas in a certain hallway. Apparently there baby scorpions can also drop Jelly Blobs as well.
Lizard Tail - These things are annoying to harvest, but they can be acquired from beating Lizalfos and Dark Lizalfos. These enemies are easy to come by in the second dungeon of the game. You only need 8 of them for all the upgrades. (I like to use them as a Flail. :U )
Edit: Since they are dungeon-only enemies, you will need to go to the second or sixth dungeon in order to find these Lizalfos. Although, it's recommended if you take on the weaker ones, since the Dark Lizalfos not only deal a lot of damage, but will also lay a "curse" on you where you cannot use your items or sword for a short amount of time.
Monster Claw - These things are as common as the Jelly Blobs. They can be acquired from beating several Keeses in caves. Which the cave can be found in Skyloft. Really easy to harvest, as well as for the Jelly Blobs. You only need 18 of them for all the upgrades. (Looks kind of boring...)
Monster Horn - Not the sharp-looking horns, but the ones you use to call or summon. Anyways, these things are really easy to harvest. If you have the Whip from the Forth Dungeon in the game, then all you need to do is steal the Monster Horn with the Whip. Not only you get to keep the horn, but it also ceases the Bokoblin Captains from summoning even more Bokoblins. You only need 8 of them for all the upgrades. (Now it's my turn to call in MY army! >:3 )
Ornamental Skull - These things are really easy to come by. Just defeat as many Bokoblins as soon as you see multiple of them. But there is a good chance of acquiring a Golden Skull while harvesting the Ornamental Skulls. You only need 12 of them for all the upgrades. (Boring looking thing...)
Tumbleweed - These things are really, and I mean, REALLY easy to come by. And they are also fun to acquire. They can only be found in the Lanayru Region and found strolling in the open-wide desert. All you need is the Bug Net (or the Big Bug Net) so you can catch as many Tumbleweeds as you want. You only need 13 of them for all the upgrades. (Um... I have no idea why I picked these up anyways.)
I hope this helps you treasure hunters get all the possible upgrades. It never hurts to get more than what you needed, right? :P