In many games in The Legend Of Zelda series, glass bottles are extremely valuable to Link, he usually can only find about 4 of them each game and it requires searching the farthest, most remote places on Hyrule. Yet there's frequently a thriving milk industry, and potion sellers can't only be selling to people who have traveled past the Lost Woods to get the one glass bottle that Farmer Brown is only willing to give to someone who completes his mini-game.
You don't need (usually explicitly magical) glass bottles to drink potions or milk...except you do because the game won't let you use anything else.
Conversely, gems are commonplace and can be found lying around in grass.
Likewise, getting an "adult's wallet" that carries more Rupees seems to always require fantastic feats and gifts from supernatural creatures. This despite Link's apparent Hyperspace Arsenal/Bag of Holding inventory.
It's the same with larger quivers and bomb bags. Although in the case of the bomb bag, several games state that they're crafted by Gorons and made of odd or rare materials like dodongo stomachs and/or the woven fibers of bomb flowers.
While the only bow in the land is always locked in a dungeon, shops still sell arrows and enemies with bows still exist. There's even a market catering to people with bows, in the form of shooting mini-games. Though this one was partially justified in The Legend Of Zelda Twilight Princess, where its heavily implied that the Hero's Bow is unique and magical.
In The Legend of Zelda: Skyward Sword, a sidequest involves a ghost on the toilet asking for "any kind of paper". Despite there being a lot of books and paper pieces in the classroom, as well as several rather pointless paper notices you can read on the wall, the only piece of paper you're allowed to give is the love letter a classmate asked you to give to a girl. And no, after the girls shoots the letter down you're not getting it back.
That ghost already appeared in Majora's Mask. And you can give him a love letter too, except the love letter here could also be used to start That One Sidequest. Thank god you can Time Travel in that game, right?
Speaking of Skyward Sword, the rarity of glass bottles (one NPC equates being allowed to keep one as adequate reward for saving his sister's life) is actually justified this time around. Glass is made from sand, sand is crushed rocks, and the Floating Continent everybody lives on has an alarmingly finite amount of habitable land as it is. Breaking any up to smelt glass (which can easily fall from the island or shatter into uselessness) would have very permanent consequences.
...and yet, the Potion Seller gives you a free bottle the first time you visit, as an incentive to shop there. Bottle can't be that rare if she's giving them away.
Though there are only like, 20 people in the whole world (as far as she's aware) and if none of them own bottles then she's pretty much out of a business.
Castlevania: Portrait of Ruin has one Guide Dang It example - the longsword. A simple weapon, probably obsolete at the time you pick it up. What takes this from oddity to hear-tearingly frustrating is that while these were as common as you'd expect in other Metroid Vania games, there's only one here, it's necessary for a sidequest (and with only 5 available at a time, you want to complete these), you won't know this until some time later, and there's nothing stopping you from selling it.
An interesting case with Donkey Kong. In the Donkey Kong Country CG cartoon, the Crystal Coconut was a rare and powerful artifact that the bad guys were trying to steal. In Donkey Kong 64, it's not all that hard to acquire a large number of them, as you use them to access special abilities.
In Maniac Mansion and its sequel, Day Of The Tentacle, nothing physically prevents you from leaving the Edison Mansion, which causes some Fridge Logic when considering the ludicrous lengths you have to go through to get commonplace objects such as an envelope and stamps (in the first game) or a bottle of vinegar (in the second). Possibly justified in that both games are set at night, and the mansion is in the middle of nowhere, possibly hours away from the nearest shop.
Granted, The Perils Of Akumos takes place on a space station, but you still go to odd lengths to find a used coffee cup.
The entire Interactive Fiction game Curses! is about the main character trying to get a Tourist Map of Paris. It turns out to require breaking an ancient family curse and time traveling several times to obtain.
First Person Shooter
There is only one Fetch Quest in Left 4 Dead 2 - and that's to get a gun shop owner a six-pack of cola. (Oddly enough, the corner store where the cola is located has only the cola in it - all the shelves are bare.)
This is also the goal of the "Hard Rain" campaign - fight your way through zombie hordes, a sugar mill full of witches and a hurricane to get gas for the boat. Justified in that the closest gas station had already been emptied by people fleeing by car.
In Far Cry 2, one mission requires you to go to a diamond mine to steal some dynamite, which you're told you'll need to destroy a water pump. The only practical way of getting the dynamite is killing all of the mercenaries guarding the mine, and there are at least a dozen of them, meaning that this little fetch task inevitably turns into a full blown firefight. This all seems very pointless, since you have RPGs, hand grenades, improvised explosive devices and M79 grenade launchers available at this point, and any one of those should have had no trouble with the fragile-looking pump.
From Team Fortress 2 we got the (in)famous hats, which are the most demanded and valuable items in the whole game despite not having practical use besides looking cool. How rare are they? With the current item-drop system, there's a minuscule change (1 in 128, possibly even lower) that you might get one after 15 mins. to 2 hrs of play, but most of time you'll get a random weapon. However, there's a weekly cap for dropped items, (roughly 7 - 12 per week) after which you'll not get new items until next week. You can also use the crafting system in order to get one, but it takes from 54 (to craft a random one) to 75 weapons (to get a class-specific one) in order to do so, which translates into several months worth of game-play.
While a lot of specific hats are rarer than others and cost a hell of a lot more metal than it is to craft them, special mention goes to the Ear Buds. These are a pair of Apple iPod Ear Buds that are barely visible on your character. Their price is equal to several dozen expensive hats (keeping in mind the above, where several months of playing may land you just one hat).
In one of the vending machines in BioShock, a cream-filled cake is around $90 despite it being found on the floor anywhere. This was done to show how without any capital control the companies could charge whatever price they want.
Fallout 3 has this on occasion, a Justified Trope in that most of the items you find are ruined. Regardless, you'll find yourself painstakingly searching through an entire library for books or through an entire supermarket for food.
Any dedicated NetHacker will tell you that two of most useful items in the game are: a magic marker and a can of grease. Both are disgustingly uncommon. *
Another inexplicably uncommon item: shirts. T-shirts and Hawaiian shirts have no armor value in and of themselves, but can be enchanted to give a valuable extra few points of protection. If you can find one. Wishing or polymorphing may be necessary.
Not all that plain, because they have charges. Can be polymorphed into something more useful or sold in some stores.
Money is surprisingly rare in The Binding of Isaac. Playing a slot machine until it explodes will sometimes give you a dollar, and there's no other way to get one. However, the most expensive items are in the realm of 15 cents, so if you do get that dollar, it'll probably last the entire game.
The world of Maj'Eyal is apparently chock-full of artificers, master craftsmen, etc, seeing as mundane items are quite a bit rarer than items with special powers. Normally, you wouldn't want a plain item anyway, as the "egoed" items are strictly better, except that gems can be taken to master jewelers to imbue mundane rings with special powers (one artifact, the Lifebinding Emerald, is totally useless without a voratun ring to set it in, unless you're playing one of the two classes in the game that can use it directly), and a pair of artifacts can transform plain weapons and armor into powerful "crystalline" versions of themselves. Especially painful for dagger users: The Crystalline Voratun Dagger is one of only three top-tier artifact daggers in the game, but the "regular" voratun dagger you need to make it is harder to find than most artifacts.
Role Playing Game
The "larger wallet" phenomenon occurs again in The World Ends With You where the only way to construct the third wallet requires Orichalcum and Dark Matter. That's some wallet.
They're also extremely rare if you waste the few you get as a part of the story. You can only obtain Dark Matter (or its trade material Shadow Matter) from some of the hardest enemies in the game.
In Puzzle Pirates, black clothing is very valuable, as black dye can only be obtained by pilfering kraken's blood, a rare resource, from strong merchant ships. Nope, you can't kill a kraken yourself, much less mix different colors of dye together.
This actually makes sense, considering that no matter what proportion you mix different colors dye together, you'll only ever get a really dark shade of brown, not black. The only way to get black dye... is by mixing a black pigment with a solvent.
An even worse example involving dyes is Guild Wars, where dye of ALL colors are only obtainable as entirely random world drops. There's a "dye merchant" but he only carries what other players have sold to him and his prices depend on supply and demand. Naturally, this means more popular dyes are much more expensive, and of course the most expensive here is also black. The best part is that dye doesn't actually do anything other than change the color of one of your pieces of armor. This is in no way surprising however, as top-quality gear is very easy to obtain, and the only things of any particular value for experienced players is gear that looks particularly nice.
Ancient proto-MMO The Realm had similar dye issues for some of its early versions.
This is actually quite realistic in pre-industrial settings. Purple clothes were a status symbol in some places.
The same 'dye is inordinately expensive' paradigm holds true in Ragnarok Online, where the only way to obtain it is to get a Mad Scientist to create the base materials, then colour them with patently absurd numbers of herbs. Players, naturally, go through the whole rigmarole in order to obtain Nice Hats.
In Final Fantasy Tactics A 2, ribbons are stated in one of the quests to be made from pieces harvested from a species of malboro that is specifically bred to make those ribbons... so the low amount of materials is understandable.
So that's why the Ribbon can prevent every status effect in the game and possibly prevent AIDS. It's made from it.
This is not your little sister's Purity Ribbon.
A mid-level quest in Dragon Quest III requires the player to travel halfway around the world, loot an ancient pyramid, and rescue a shopkeeper's daughter so that said shopkeeper will bestow upon you some ground black pepper.
Considering that historically spices were occasionally worth more than gold by weight... it makes a certain amount of sense that someone with the resources of a king might trade something that isn't irreplaceable (a ship) for something that, in that part of the world, was practically one of a kind...
The world in the game is (deliberately) modeled after medieval-era Earth. The king of Portuga (Portugal) wants you to go all the way across Europe and most of Asia to get him something that has never been seen in his area before. Which is similar to how the spice trade of old worked.
A more bizarre example exists in Dragon Quest IX. Early on, you'll run across a sidequest to help make medicine out of the famous cure-all water of Angel Falls. The man who makes the medicine requires "fresh water" to make this medicine... which you won't be finding for several hours, five towns later. Turns out, by "fresh water", he means the alchemy ingredient you can find in predetermined spots on the world map. According to the item's description, the "fresh water" is "wondrous" and of "perfect purity", but when you're asked for "fresh water", you don't expect that to turn out to be a mid-level alchemical treasure, do you? (Special mention also goes to another alchemy ingredient found only on a few enemies, or in a single gathering area on an island... kitty litter.)
Dragon Quest VIII has a Commonplace Rareship. You need a ship, so you need to find an ancient abandoned ship in the desert, then go through a monster-filled castle to find the library, then get a once in a lifetime wish and give someone a priceless ancient artifact owned by a king who owes you a favor, to put the ancient ship in the water. Why you can't just ask the king for a ship remains unexplained.
In Kingdom Of Loathing, many kinds of fruits suitable for cooking and cocktailcrafting can be bought from NPCs for 70 meat, but others like cherries, limes, and jumbo olives can only be found as loot on monsters, so they go for roughly 1000 meat at player-run stores. Bananas are limited-edition fruits that sell for around 30,000 meat. However, this is nothing compared to beets, which were discontinued so long ago and dropped so infrequently that they can't be bought for less than 130,000,000 meat, despite being completely useless note Its description says "...a beet cannot be beaten. Or beeten." They left out "Or eaten." Yep, the most valuable food in the Kingdom isn't actually food.
Pickling supplies (dill, brine, vinegar, and ghost cucumbers) are quite rare, as the area where they drop only appears for a single day at a time, completely randomly. The factory has only appeared 6 times since June of 2004. Holiday monsters also create some common-rares; Thanksgiving foods (tofurkey, stuffing, cranberry sauce) can only be acquired once every 3 months, and each player only gets to collect a few of them.
The Tiny Plastic Sword is Exactly What It Says on the Tin. It's used to make top quality drinks with relatively little investment. They are sold at the mall for 44,000,000 meat.
For reference on what these prices are to people who don't know the relative value of money in Kingdom of Loathing, the Mr. Accessory item (Which players recieve for each $10 they donate), sells for ~11,000,000 as of this edit (The price fluctuates depending on what goodies you can exchange them for). That's right, tiny plastic swords are worth a little bit more than $40, and beets are worth over $120.
There is also Hell Ramen, a food whose joke is that Ramen is so cheap, you gain money by eating it. Except it is very good food, so it goes for a few thousand meat in the mall.
Used wrapping paper (which can be crafted into equally-rare weaponry or used to make gifts with nothing in them) costs 120 million meat—that is, $80-100 of real-life money, or many months of meat farming. It was only available from gifts in a Crimbo giveaway back in 2003 (more common gifts from later on don't produce the paper item when opened), only a few were generated because there weren't many players at the time, and most of them have been lost over the years due to account deletion.
In Runescape, party hats are some of the rarest, most expensive items. What is a Party Hat? A crown made of colored paper. There are also discontinued holiday healing items that are rather valuable, such as pumpkins, Easter eggs, and the most valuable item in the game - Christmas crackers. Half-full wine jugs are also ludicrously expensive (originally, you drank half of a jug of wine at a time, but they later changed it so your character chugged the whole thing).
The quest "One Small Favour" will take at least four hours of dedicated running around the map doing errands for a huge number of people for an incredibly unique item: A keyring. A small band of steel, bars of which most players have sitting in their banks, which even the universes greatest blacksmiths cannot replicate.
That one is justified. The quest starts with you doing the titular favor of running outside of town to get some special logs. The guy who has them needs you to take his axe to get sharpened. The guy who does that won't do it until you can convince a lady in Draynor Village to testify for his friend, and so on. When you finally complete the initial task, you only then find out your reward is the keyring. The shopkeeper doesn't know why you were expecting a bigger reward for doing "one small favor".
In World of Warcraft, after leveling your character up to level 45 or higher, you and a group of 4 other like-minded adventurers (you'll die if you try to do it alone) can go on a dangerous quest deep inside Zul'Farrak to obtain the electric scale of a giant hydra named after Godzilla. To simply summon this hydra, at least one of your group must go to another continent, then battle his way through hordes of troll cultists to obtain a sacred mallet, then battle his way through even MORE hordes of trolls to bless this mallet at a very special altar. AND all those trolls used to be elite, that is extremely powerful for their level (thankfully, they changed that in a later patch). Your ultimate reward? A carrot on a stick. In the game it actually was rare and highly sought-after for a while because it was one of very few ways to make a mount go faster, but the mundaneness of the item itself made the whole quest chain absurd. The absurdity was only compounded by the item being usable with any mount, include carnivores.
This makes this item a subversion, since a carrot on a stick that can motivate a meat-loving tiger to move faster is obviously magical.
There also exist a lot of items you can buy from vendors that are incredibly expensive while serving no actual purpose whatsoever. Unless you happen to need, say, a wedding ring for roleplaying.
Some kinds of pets are incredibly rare to acquire. Rats, for example. Some others can only be bought from vendors of one faction, so they will be fairly expensive for players of the other faction wanting to buy them over the neutral auction house.
While on the topic of Warcraft, the orc campaign in The Frozen Throne, has you go on a sidequest to retrieve a powerful artifact, as part of a shaman's dying wish. You get to keep the artifact, and are also rewarded with a unique item: The shaman's weapon which is like the one every single shaman owns. Its only power is to give your attacks a lightning damage bonus, which makes it no different from an ordinary lightning orb.
Earthbound, since it takes place in an Urban Fantasy instead of medieval times, is full of them. Made more obvious by the fact that prices are based on their value in yen, yet in-game currency is dollars, leading to a $3480 frying pan and a $98 cup of noodles.
A similar thing happens in Dead Rising 2, even the most trivial items (snacks, slot machines, etc.) cost almost $100. Although just liked stated above, if you were to move the decimal 2 places the prices would make more sense.
In Pokémon Gold and Silver , a road is blocked by a 'tree' (actually a Pokémon, Sudowoodo), so nobody can pass there. You have to defeat the (difficult) Gym Leader in order to acquire an item that will allow you to remove said tree: a Squirtbottle. (Sudowoodo is actually Rock-type, making it weak to water).
Introduced in the same game: Charcoal. While this game allows you to buy an endless number of them, future games (and even the remakes) don't and give you a single piece of Charcoal per game.
Fishing Rods, which are only available by finding three specific expert fishermen on your journey; in Black and White and Black 2 and White 2, you don't get any rod until post-game.
In Pokemon Red And Blue, a bicycle costs 1 million Pokedollars (you can only have up to 999,999), but a short while later in Vermillion City, you can get a free bike voucher that allows you to get the bike.
Soft drinks probably qualify for this, since apparently only one town per region (except Unova) has vending machines.
The Pokemon Audino in the fifth generation — it can be tough to find if you don't know to look for any shaking grass (where it has the highest percentage of showing up in later routes).
Lands of Lore 2: The silverleaf is supposed to grow in the Dracoid Cemetery. Except that it doesn't. Instead, you have to find glass orbs, charge them at three different machines (One of which is located in a completely different and HUGE level, the Dracoid Ruins) to open the various crypts. (The orbs can be charged with white, blue or yellow sparks to open crypts with corresponding doors. If you you don't have the right kind of orbs, you may have to go all the way back to the right machine.) In one of those crypts you will find the ghost of a dracoid priest who wants you to cremate his body for him and bring him the ashes. And where might his body be? In the farthest corner of the Ruins. So after this incredible endeavor, he opens the door into the dracoid king's crypt for you. (This is back at the Cemetery, mind you.) What does his ghost want? To destroy what's left of the Ruins of course! So he gives you his bones in an urn that you have to take to a statue somewhere in the ruins, which will come to life and fight an ice worm, causing the ruins to flood. So you have to get the hell out of there, end up back in the jungle, head back toward the Cemetery... and then the king will make the silverleaves grow. AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAARGH!!!!!! And to top it off, whole piles of silverleaves turn up later at the Ruloi Citadel.
At one point in Beyond Divinity a dying prisoner asks for a drink of water. You have to go back almost to the start to get the only bottle of water on the level. This takes you through a guard station, mess hall and kitchen area but none of the dozens of cups and bottles contain any water or can be filled from the numerous barrels and sinks.
Secret of Evermore has the alchemy system. Oh, sure it makes some sense to have trouble gathering things like Oil, or Wax, but... water? It's not even like it has to be purified water, you can literally scoop it from a river in the middle of a swamp. But only in certain spots that are sniffed out by your dog.
In Star Ocean 2, you have to go into a dangerous cave filled with monsters as a test of strength - the proof of your journey being to bring back a rare and undiscovered herb. It turns out to be clary sage, a fairly common, hardy and widely-distributed medicinal plant. Still, everyone reacts as if it was incredibly rare.
On the other hand, you're explicitly not on Earth in this scene—you're on the planet Expel, where Clary Sage very well might be a rarity.
If you want to go the extra mile, however, you can go further into the cave and find the Dill Whip. This doesn't bring you any reward whatsoever, but at least you get told that your characters have found a legitimately undiscovered plant.
Chrono Trigger has jerky, which appears twice in the game. The first time it is used is as a minor plot advancement point. The second time it is part of a Chain of Deals for getting some optional equipment in one of the zany sidequests. About 2 minutes into the game you can find the shopkeeper selling it, for 9900 gold. A trifling price when you will need it (much later in the game), but at the beginning it seems insanely overpriced.
Bizarrely, you can also resell the Jerky for 10,000 gold to the person you're supposed to give it to. However, to advance the plot, you have to give them the Jerky for free.
Backpacks, of all things, are some of the rarest, most expensive goods in Ferelden.
In Ultima VII Part II: Serpent Isle, one of the common reagents you use for spellcasting is mandrake, and indeed it can be found and bought in plenty of places. Later in the game, an NPC gives you the task to obtain mandrake. For some reason, only mandrake from one specific location qualifies, all the other mandrake doesn't work; and you can't get to that spot yet (semi-justified in that he wants fresh mandrake, and the stuff you can buy is presumably dried: it doesn't make a difference a spell reagent, though).
Going back further in the series, in Ultima IV mandrake and nightshade cannot be bought, and can only be harvested in one place each in the entire world, during one particular lunar phase.
Guns in Resonance Of Fate are like this. One can only wonder where all the hordes of bandits in the Random Encounters get their guns from, when only two handguns are for sale in the entire game, both at exorbitant prices. And yes, that means two individual guns, not two types of guns. Naturally, the hordes of bandits never drop their weapons when they die either.
It's not quite this trope, but in The Elder Scrolls V Skyrim, without mods there is no way for you to do fletching of arrows (despite at least one NPC being explicitly a fletcher). You can purchase arrows from various shops, and naturally enemies who carry bows will have arrows on them... but using smithing skills you can make Daedric armor but not a stinking iron-tipped arrow? (Fortunately a very nice mod takes care of this.)
Arrow making is officially added in the Dawngaurd DLC.
On the subject of Elder Scrolls, in The Elder Scrolls III Morrowind, there is only one muffin on the entire island of Vvardenfell. And it already belongs to someone, so the only way to obtain it is to steal the delicious baked good. And if you eat said muffin, it gives you the exact same stamina regeneration as a normal, common piece of bread.
A couple of the forging items in Dissidia: Final Fantasy. For example, you won't even be able to acquire any variety of wood until after you've beaten Chaos - which involves defeating ten characters' personal stories, plus four additional stages of battle (all of which have five substages). Even then, one slab of regular lumber is apparently more common than a splinter (and explicitly costs less to trade for).
Though not rare per se, it takes a lot more effort to find a human bone in the catacombs in Planescape: Torment than it really should.
In the Playfish game Restaurant City, ingredients are ranked on a scale of one to five stars, with five being the most expensive. However, the stars are handed out based on how many recipes use them, with the result that sugar and eggs are five stars, while saffron only has two.
Tactical shooter 7.62mm High Calibre, there are several guns that are extremely hard to find, and several guns that are extremely easy to find, based on both how far you are in the game's plot, and who you're buying from. On the other hand, ammunition can be absolutely impossible to find. At the beginning of the game, 9x19mm Parabellum bullets, one of the most universal rounds used today, cannot be found anywhere, while 7.62x25mm Tokarev rounds, which are designed for weapons that are barely even produced (the TT-33 Tokarev and the Skorpion submachine gun being the most common weapons to use the round), can be purchased in bulk. Later in the game, you might be struggling to find enough ammo for your common 5.56mm assault rifles, while tripping over Gyrojet rounds and 5.7mm pistol clips.
To give an idea of how ridiculous this is: the 5.7x28mm round is used by only two weapons in the entire world (the Five-seveN pistol and the P90 PDW) and aside from all models of the Gyrojet being rare collector's items, so is the ammunition (selling for over $100 a round). The 5.56mm, on the other hand, is the standard rifle round used by NATO. 7.62x25mm Tokarev rounds genuinely are common, though, given ridiculously vast stocks of Soviet and Eastern Bloc surplus ammo that was exported to America after the fall of Communism.
Turn Based Strategy
Jones In The Fast Lane: The prices in the Monolith Burger are weird—a cheeseburger for $89, fries for $65, shakes for $103... That said, each of these fills you up for an entire week, so it probably shouldn't be taken literally. (Though it implies that you've been living on nothing but milkshakes the entire week... This cannot possibly be healthy.)
Wide Open Sandbox
In Assassins Creed II, enemies use the same weapons that you can buy for large amounts of money from a shop. Pretty generic example, except- you can pick up the weapons. But you can't keep them of course, if you try to switch weapons, it just drops the thing.
You actually can keep them if you've been disarmed, usually by an enemy with a two-handed weapon. Said two-handed weapons do fall into this trope though.
This is justified, as they are too big to carry while free-running.
You will also find that to carry more throwing knives or phials of medicine/poison you will need to buy pouches. These can cost 6,000 florins, more that it costs to buy finely crafted weapons or armor, and can even outprice the extensive repair and refurbishment performed on the buildings around your villa.
Appears with most of the mid-to-high tier items in Animal Crossing. Items of the highest rarity level can be reliably earned at the game's special events. But the items just below that level can't be found at special events and only appear as very rare common items. As a result it is far, far easier to, say, earn the king and queen of the chess set than it is to earn the rook or bishop.
In Minecraft, like in the Adventurers! example above, apples used to be incredibly rare. Rarer than diamonds. So are leather saddles (which you can't craft from leather found commonplace).
Apples were so rare that, without hacking or using mods to get apples, the only legit way to get an Apple was to kill Notch if playing with him on a server. It wasn't until the 1.8 patch that added strongholds with chests that have a chance of carrying an Apple or more. Since the full game was released, apples fall out of trees when you cut them down or destroy the leaves, but they only have a 1/125 chance of falling from any given leaf block.
Clay was also rather rare in the earlier days of the game, only available on coastal areas. Make a boat and get to searchin'!
As a matter of fact, Clay is a strange example of this, as it's rarer than diamonds, but easier to find. There's a decent amount grouped near water, but only near water. Diamond is just really really deep and spread out.
Watermelon seeds and Vinyl records are only found in treasure chests deep underground, making them among the rarest items in the game.
Cookies were this for a long time, to the point that they became a sort of trophy. This changed once cocoa beans became farmable and could be easily found in jungle biomes, instead of just in dungeon chests.
As mentioned in the Yahtzee quote, making a cake is a highly elaborate process: you must build a furnace and a stone or better pickaxe, find nine iron ore, smelt them into nine iron ingots, make three buckets, milk cows, grow or find wheat, gather sugar cane and make it into sugar, and find an egg laid by a chicken, then put them all together. That said, once you get to the point that you can produce one cake, it becomes fairly easy to make more.
Carrots and potatoes are also pretty hard to get ahold of: you can only find them growing in NPC villages (which themselves are rather rare) or as a Rare Drop from zombies.
Name Tags, the only legit way to give any mob a unique name outside of creative mode, can only be found inside chests located within a dungeon.
In Scarface: The World is Yours it's entirely possible to have lackeys wielding weapons the player is not yet allowed to buy. Don't fret. They can give them to the boss by placing them in the trunks of special cars (think mobile armory). Doesn't quite work with the boat-mounted machine guns that Tony can later buy to wield himself. Also, it doesn't quite matter how much cash Tony has. Being able to purchase entirely legal items (such as a vending machine or a park bench) depends on how much his enemies respect him.
In the X-Universe games, microchips are everywhere — weapons, ships, components of all kinds. And yet, good luck finding some in the universe — there's so much demand, and the production process involves such a convoluted chain of supply, that most chip factories are permanently empty — the few chips they produce are instantly snatched up by NPC traders. And if you do manage to be faster than the traders, expect to pay ludicrous prices for them.
Oh, and you need to gather 75,000 of them for the last stage of the Hub plot. Good thing you can build your own Chip Plants, or else this plot would be next to impossible.
Non Video Game Examples
Real Life gaming example: Yu Gi Oh, aside from the regular rarities, actually has two "Short Print" varieties of the Common rarity cards; they look, act, and essentially are exactly like regular Commons, but you'll be busting your butt and your wallet going through hundreds of packs just to get one.
In the online game Neopets, the rarest items initially were... food. The only place food was generated was at the food stores every five minutes. Unfortunately, they ran out in 15 seconds or so. You could feed your pets at the soup kitchen if you were poor enough, which led to lots of people in Perpetual Poverty just so they wouldn't have to spend all their money on an apple.
Not to mention some of the rarest and most coveted items on the entire site are merely paintbrushes. Granted, they're magical paintbrushes, but...
A debatable, entirely non-gaming example: diamonds, at least according to this article from the 'Atlantic Monthly'' in 1982. This is less the case now since the De Beers corporation, while still retaining significant market control, no longer has a monopoly on diamonds. The pricing is still rather high given their actual commonality (it's been said that you could give every living human a cupful of them, though not necessarily the highest quality ones).
In the Paranoia RPG, the ability to recolour equipment which is above one's security clearance (and therefore punishable by death to possess or be seen using) to a colour you are cleared for (and therefore make the gear usable) is very important. Not least because stabbing each other in the back is the whole point of the game, and a low-clearance RED laser, for instance, will be defeated by not-quite-so-low-clearance ORANGE body armour. Since players are usually RED level, this is more useful than one might initially think. This results in paint being one of the most restricted types of item in the game. Other items requiring high security clearance include really powerful weapons like cone rifles and plasma generators, but also some things that are utterly mundane in real life, like chapstick and umbrellas.