My Sleepy Peasant Village!
All to often, characters come from a village that was destroyed and they are likely the sole survivor. While in rare circumstances this is okay, more often than not it is simply a set up for a revenge based character or a cop out for lacking a suitable history. Villages are not razed to the ground on a regular basis, unless your campaign is set during the Black Plague when entire villages did perish to said plague, or during massive migratory invasions, like the Huns, Mongols, or Vikings moving through an area pillaging and destroying. In the first case, survivors are thought to be tainted with evil, and in the second they are made slaves by the destroyers.

Middle Age at 12
Another painful cliche is the constant youth of many PCs. The late teen years seem to be ideal for characters with years of martial training and experience, and anyone over twenty, or *gasp* approaching thirty is tired old mentor ready to held the PCs. It was common for teens to be seen as adults during older times, with weddings coming soon after puberty. This was not a testament to the ability of said teens, it was the cold fact that 40 was considered to be the oldest that many survived and society could not let people spend half their life as unproductive members of society. Such young characters would be as unsure, inexperienced, and uneducated as teens of the same age today.

Little Orphan Annie
As a corollary to the destroyed village, entirely too many PCs are orphans, their parents killed by the plague, the war, assassins, bandits, bad salmon, car crashes and the like. Often this is little more than a cop-out to having a developed past, or a reason to play a moody loner character. In the medieval era, most orphans were given to the church and were raised in monastaries as opposed to the Dickensian orphanges of street scamps and urchins.

Obligatory NPCs
GMs are just as guilty of cliche crimes as the Players are.

The Spunky Princess - There will without fail be a princess or other female lead who refuses to accept the role of her gender and social station, often without real reason.

She-Rambo - The standard Amazon warrior, often decked with scars to prove that she is just as good of a warrior as the next man. Often expresses a man-hating attitude but invariable falls for…

The Big Softy - Giant flexing muscles, tattoos, scars, big scary weapons, a gruff demeanor, but underneath the hard exterior is a heart of gold.

The Handsome Villian - often with waist long hair, cool voice and deadly moves, can be a high ranking lieutenant, or the supreme evil himself as a disguised demon (yawn) or other evil. It is really Sephiroth’s fault for this one.

The Keystone Cop - Painfully incompetent, this lieutenant to the villian couldnt shoot the broad side of a barn and falls for even the most sloppy disguise. In a lesser vein, many henchmen and stormtroopers fall into this cliche.

Mr. Annoying - Opposite of the Keystone Cop, Mr. Annoying survives every encounter, always has the upper hand, and is the focus of character hatred. Not because he is a recurring villian, but because he remains untouchable no matter the PCs efforts, no matter how clever or ingenius.

Sword at a Gun-Fight - The sword is the greatest weapon ever made. It can deflect bullets, cleave through any armor, and even perform ranged attacks. Don’t believe me, watch any mecha anime and swords will always deal more damage than any plasma cannon, nuclear detonation, or cosmic ray generator. In real life, swords started loosing their effectiveness as armor improved in quality. The best weapons for fighting armored foes were hammers, maces, and heavy piercing weapons, nto big knives. The military has ceremonial swords and fully functional guns and cannons.

Kidnapping
While bieng surivors of a destroyed village and parentless, the PC will have two siblings, one older and one younger. The Older sibling will have fallen to darkness to become a henchman of the main villian while the younger sibling will be constantly kidnapped and held at threat of death.

to Hell with Altruism
Even when the PCs are facing down a terror that will destroy the world, the city, etc, vendors will not help the PCs but rather demand their normal prices for weapons, supplies and goods no matter how mundane. In exchange for defeating said foe or menace the PCs are later given a weapon or magic item that would have been ten times more valuable in fighting the monster to begin with.

We don’t need no stinking building codes
Every building no matter how old, new, large, small, important or insignifigant is riddled with hidden passages, Egyptian pyramid style traps, and corridors that lead to long forgotten and lost dungeons and catacombs under the building. While there are certainly building with hidden passages, they are by far the exception to the building code and catacombs and dungeons are major excavations, not something that is quickly and easily done without anyone knowing about it.

Ultimate Weapon - Unless it is vital to the story, a weapon never jams, breaks, needs sharpening or any other maintenance. Incredibly potent weapons are much more likely to break or fail than the normal broadsword purchased from the blacksmith in the last town. Unfortunately in real life, swords quickly become dull and sword on sword combat is a sure way to ruin a blade very quickly. Armor needs to be repaired, blades need to be polished and oiled, and arrows are seldom good for more than one shot.

Nobody is paying attention
It is perfectly commonplace for a band of warriors and mages to come galluping into town clad in armor, draped with enough weapons to arm a peasant uprising. It is even acceptable for said warriors to turn a common room at an Inn into their HQ for the time being. In medieval times, weapons and armor were regulated by the nobility, they didnt like the idea of the peasantage being able to properly arm and armor themselves. Sherrifs, city guard and the like were as much about disarmament as about keeping the law, arresting thieves and the like. During that time, the main concern of law was maintaining the status quo of nobles on top, peasants on bottom.

Eat your heart out, Nostradamus
Every single prophecy ever written will come true, likely exactly as it is written. And chances are, these events will be centered around the characters and the current day. This really clashes with prophecies from the real world as they are wrapped in symbolic imagry and most never actually happen, or are so vague that the events listed could have already happened a dozen times over.

The Collector
If five talismans, 12 zodiac stones or any other number of items are mentioned, you can bet you are going to have to hunt down each and every one of them. As a corrollary, these items will require lengthy side quests, thefts, and the last one will have been on one of the characters since the begining of the game as a family heirloom/trinket.

Simple Geography
Every country is limited to a single city, with sole exceptions being a border fortress three times the size of the capital. The PCs home country will defy this rule and have 3 cities. During the medieval period, 95% of the population lived in communities of less that 1000. While cities were indeed rare and generally far between, the web of thorps, towns, hamlets, and villages between them made travel not quite the Western-esque romp through the wilderness.

Monks Always Know Kung-Fu
Somewhere along the way, the martial artist monk of the East replaced the ascetic monk of the West. While there is nothing wrong with Kung-Fu monks, not all monks know kiai strikes and chi manipulation. Many wore a shaved head, carried books and acted much like Clerics.

The Law of Embargo
Anything developed in one city/kingdom will only be available in that kingdom. Trade does not exist in any form other than the PCs giving GP for new items and stuff. The event that ended the Dark Ages and kick-started the Renaissance was trade of ideas. The ideas were brought back from the Holy lands and the far east by crusaders returning home. These ideas grew and were traded back and forth until the squallor and filth of the Medieval was replaced with the new age of the Renaissance. While the spread of such ideas is as repugnant to most static-minded DMs as the intrusion of gun powder and guns into their games, this was not an overnight change, instead it took decades and centuries to come to full fruition.

The Inverse Law of Mecha
No matter how primitive the setting, there will be giant robots.

Purchase and Pennies
There will only be one shop of each variety of a city, one weapon shop, one armor shop, one inn. No matter how far flung these various cities are, they all accept the same currency without a blink. Of course the exception is the ‘hidden shop’ that has the most secretest and awesome of goods. While there were guilds that controlled the flow of commerce in a city, they were self governing bodies dedicated to price and quality control, not monolithic corporations. A city coud have hundreds of cottage workers making belt buckles and hats down to half a dozen inns or more depending on the population. Currency was also variable and negotiable. The currency of bad nations would be less accepted outside of those places, while powerful kingdoms would have more valuable currency.