Tokyo_Bunny_8990: Yeah my first thought was the Merchant from RE4 (great quotes, will stop appearing in a specific location if you kill him in that location on Professional difficulty, and doesnt sell if there are enemies that occurs in one location). The mystery comes from the fact that the merchant himself is also infected by las plagas but is not mind controlled by the big bag.

Goes into fan theory but the shop keeper in Slay the Spire. The game itself is quite mysterious (your character is tasked with slaying the spire but we dont know why asaik but the "cards" are implied to be memories/a UI for the player to choose what moves the character will do in battle. The merchant can sell these cards which means the merchant can arguably be teaching you these moves.

maxleod: FFS. Nobody mentionned Stan? The STAN???

dtgreene: Hummingway merchant in Final Fantasy 4.

There's a cave, on the moon, which is filled with a bunch of Hummingways, all of which look exactly like Namingways. Most just hum when you talk to them, but one of them will open the shop menu, allowing you to buy consumable items including Elixirs and Whistles. (Be aware that Elixirs are *expensive*!)

There's also an actual Namingway living among the Hummingways. (In 2D versions, he offers to rename your characters.)

Some others in the Final Fantasy series:
* FF1: In Lufenia, there's a hidden merchant, outside of what appears to be the bounds of the town, who sells Arise and Flare (LIF2 and NUKE in NES translation); I believe you can even buy them even if you haven't yet learned the language.
* FF2: The final dungeon has a merchant hidden behind the waterfall who sells powerful spells.
* FF3: At the end of Eureka, there's a merchant who sells 8th level spells, one who sells powerful summons (in 2D versions, only if you've earned them first), and a hidden merchant who sells crystal equipment and shurikens.
* FF5: There's a mysterious town, entered in what at first looks like a random encounter (in the SFC version; later versions spoil this by using a different transition for random encounters, but not for the town entry), with merchants who sell either high-end or unusual equipment.

Dragon Quest games have their share of unusual merchants, as well:
* DQ2: One of the merchants has a blank slot on the list of items for sale.
* DQ3: There's that ghost town, which is inhabited only at night. My favorite thing isn't the merchant, but rather the innkeeper; you pay for a night at the inn, go to bed, and there's no innkeeper there when you wake up.
* DQ4: That one fox merchant who lies to you. When you buy an item from the list, that's not the item that actually enters your inventory. This merchant appears in Chapter 3, and isn't the only unusual one in the chapter. There's one who you can work for, and if an item is sold by an NPC, you can buy it back yourself (including one particular sword that's rather nice for this point in the game). There's random encounter merchants. (You get into an encounter, but instead of a fight, you get to shop.) And, of course, your character is a merchant in this chapter (though I suppose that one doesn't meet your criteria).
( DQ7: There's that one bird merchant. Shopping with that merchant is like navigating the shop in a JRPG in a language you don't understand.dtgreene: There's also Tarhiel. He doesn't have anything for sale, has no money (so you can't actually sell him anything), and actually talking with him is not so straightforward, particularly since he spawns in mid-air and doesn't have enough health to survive the landing.

Think there may be some merchants in the Elder Scrolls series who start out hostile. (In other words, they'll attack you as soon as they see you.) I believe Morrowind's master Enchant trainer is one of them.

CMiq:

.erercott: I remembered!

NO MORE HEROES 3 had an eerie mysterious merchant that sells sushi as power-ups.
It's DonMai Sushi's chef. He's got a giant red skull for a face. It was really unsettling when I first met em. I thought it was a bit grotesque to have a giant head squeezed in-between two tiny shoulders, but he's one worth remembering in my book.