Secret Shop

Jake: "The entrance is disguised so you can’t find it. [...] And they don’t let anybody in without a VIP card. So don’t expect to waltz through the door by accident."
Marth: "But... how do they stay in business?"
Jake: "Who knows! Last I heard, they were desperate for customers."
Marth: "Then maybe they should reopen as a “tell your friends” shop..."

—Jake and Marth, Fire Emblem: Shadow Dragon

Most businesses follow a pattern: you need something to sell, you need people to buy it, and you need to make more money than you spent every time someone DOES buy it. This is pretty simple to understand.

But then there is that one shop, whose proprietor takes lack of advertising Up to Eleven: this shop's defining feature is how hard it is to just to get in. Maybe it's just ludicrously hard to find or get to, maybe you need a keycard or passcode, or maybe only the king is allowed to shop there naked during a full moon while holding a child's teddy bear in one hand and the Sword of Plot Advancement in the other. Maybe some combination thereof. Either way, expect getting in to this place to be harder than getting to your local department store.

So how does this shop stay in business? That would be their secondary defining feature: this shop sells the good stuff, and for lots of money. If purchasable, this is the place where one would buy the Infinity+1 Sword, some spare Green Rocks, or a Wave Motion Gun.

Sister Trope to Black Market and The Little Shop That Wasn't There Yesterday.

Examples of Secret Shop include:

Anime and Manga

In ×××HOLiC, the shop can only be seen by those who need it, and sells wishes for something of equal value.
The eponymous Pet Shop of Horrors doubles as The Little Shop That Wasn't There Yesterday.

Comic Books

The question of, "who makes every character's costume" was answered in Amazing Spider-Man #502, which introduced Leo Zelinsky. A tailor from Brooklyn, he doesn't do much to keep his business secret except what small business owners like himself always rely on - using only word of mouth to advertise - but he caters to just about every super-human in the Marvel Universe, heroes and villains alike. (Why does he see nothing wrong with this? As he explains, "If Doctor Octopus goes into a deli and orders a cheese sandwich and the clerk gives it to him, does that make the clerk a bad man? Everyone has to eat, everyone needs clothes.") To avoid conflicts between the heroes and villains, his shop is open for the first group on Monday, Wednesday, and Saturday, the second on Tuesday, Thursday, and Friday. He also maintains a strict confidentiality policy for all of his clients, only breaking it once in order to prevent a murder. Otherwise, his clients have included such big names as The Avengers, X-Men, and Doctor Doom.
The DC universe has Paul Gambi, whose shop is similar to Leo's but not seen as often, mostly in The Flash's comic. Clearly he is a Shout-Out to Paul Gambaccini .

Film

Men in Black had Jeeb's shop for special "imported merchandise"

Kay: "You sold a reverberating carbonizer with mutate capacity to an unlicensed cephalopoid, Jeebs, you piece of shit..."
Jeebs: "He looked all right to me. "

Literature

Diagon Alley in Harry Potter. To even see the front of the store that leads into the back alley that has one brick which must be tapped to get there, you need to be a witch or wizard. Or maybe a squib.
Subverted in Terry Prattchet's Soul Music.
The Merchants MacDoig in the Lonely Werewolf Girl books operate like this, if you don't where they are then you don't need to buy anything from them.

Live-Action TV

The Unusuals: the squad comes across a "Murder Store," where you can buy everything you need to kill someone. They decide to run it themselves as a sting operation.
Dollhouse
Class of 3000 had a gift shop where you had to pass through an Indiana Jones style Death Course in order to enter. It turns out they did most of their business on-line.

Video Game

The Mirage Village in Final Fantasy V. You encounter it as a random battle in a specific place.
- Final Fantasy VI has a strangely inverted example. The weapon shop in Narshe... nothing can be bought there, and Narshe is the first town you see in the game. Plus, the town is otherwise deserted, and the door is locked. However, the weaponsmith will offer to either give you a piece of magicite or forge it into a weapon.
- Final Fantasy IX has a secret synthesis shop, which you access by defeating Hades... who is, in addition to being tough to beat, also hidden in the Very Definitely Final Dungeon. Plus, you'll need the ingredients for whatever you want him to make... a few of which are unique.
- In the secret dungeon of Final Fantasy XII, there is an invisible shop in a room that looks just all the other rooms; you have to get within a few feet of it to see the interaction icon.
Some Fire Emblem games have secret shops, which are slightly-different-looking tiles of floor in out-of-the-way locations, all run by the unofficial Series Mascot Anna. You require a member's card to get in, which can only be obtained by stealing one from enemies, and the prices can be downright exorbitant. Discussed in Shadow Dragon, as quoted above - Jake, Anna's boyfriend, admits that business isn't looking so good for them because they're a secret shop.
Tactics Ogre: The Knight of Lodis has a secret shop in one of the early towns, which you can access when you recruit Deneb.
Wallace has a not-so-incredibly secret shop in the Scott Pilgrim vs. the World game. It's marked with a star near the end of the first level.
Tales of Symphonia has a rather devious one in Luin, which you must pay to have rebuilt along with the rest of the town. There, you can purchase the best weapons that money can buy for each character, and each one is a Lethal Joke Item.
The Black Market in Wild ARMs 3 sells some pricy stuff, and you need a Black Card to get in.
The Knife Guy's casino in Super Mario RPG.
The DLC location Black Emporium in Dragon Age II. Sells some of the best items in the game.
Crazy Redd's store in Animal Crossing:City Folk. You need to have one of your neighbors mail an invitation to you, and in order to do that, you need to randomly talk to them. If you don't have an invite, he'll casually shoo you away, and drops the not-so-subtle hint of how you're supposed to get in. Other than that, it's actually pretty easy to find. Only place with an iron-looking door.
Maple Story has a shop on the far side of Leafre, which you can't get into until you complete a high-level quest.
In Mabinogi, several of the regular stores have "secret shop" tabs, which can only be accessed when you become friends with the owner, or some such; these shops typically have costlier, more useful items. Plus, there are 2 NPCs who wander from town to town; finding them requires either luck, stakeout and patience, or a guide.
Some shops in The Legend of Zelda series are hidden under bushes, which must be chopped down.
River City Ransom has Merlin's Mystery Shop, which is hidden in the Armstrong Thru-Way Tunnel. It sells expensive fantasy items with names like "Excaliber" and "Zeus Wand" that provide enormous stat boosts.
RuneScape has several of these (usually involving the completion of a quest), but the prime example is the Ape Atoll; you can't shop anywhere on the island until you're done two (moderately long) quests, you will be attacked if you show up in the vicinity without turning yourself into a monkey of some kind, and you can't communicate with the monkeys unless you're wearing a monkeyspeak amulet. Also, the island itself is right on the southwest edge of the world, and can only be reached by gnome hang glider. The most commonly-bought item on the island is a Dragon Scimitar, which is a good weapon for medium-high level fighters, and cannot be purchased (from NPCs) anywhere else.
Knights of the Old Republic has a merchant on Korriban who sells some of the best items in the game, but you have to talk to his associate on Tatooine before you can get a recommendation. Unfortunately, a bug stops him from turning up if you have reached a certain stage in Juhani's side-quest.
La-Mulana has many secret Dungeon Shops that are hidden behind pots or blocks or are only revealed by using seals or Key Fairies. In a major Guide Dang It, one vital Plot Coupon is sold from a shop that only appears if you buy an obviously fake item from another shop.

Web Comics

Done deliberately in Megatokyo; when Largo is asked to watch over Mega Gamers, he installs a fully functional maze of cardboard robots and obstacles... which turns out to be outrageously popular.
In one Bobwhite Christmas story arc, Cleo learns from her younger sister Adelaide of a secret store in their hometown selling used and super-rare videogames. It's hidden behind a shady internet cafe in order to stay secret.

Cleo: I especially liked how the cartridges and discs were loose and barely in alphabetical order! Probably to discourage the noobs.