The PCs stay at an inn; when they awaken the next morning they find themselves in a ruin of an inn. Perhaps the rest of the town is also a long undisturbed ruin - or perhaps the rest of town is normal, but no one seems to find it odd that the PCs stayed in a place they acknowledge burned down years ago.
Clouds in the distance are not rain clouds - they are vaporous ... things ... swimming through the air. Every now and then you seem to see bulbous eyes within the vapors, staring back at you.
Every so often, when no one is looking at it, the moon suddenly changes its phase (crescent to full to half to new to gibbous, etc). To be more subtle, the moon is the same, but the position of the planets in the sky are different every time instead.
When the wind blows strongly a nearby cave is heard to make a sound like a deep growling moan. But if any of the party speaks draconic, they realize that the moan is actually spoken words of a ghost bound to the cave, to faint to hear except when the spirit takes advantage of the wind to make louder their voice.
You see what appears to be a ghostly re-enactment of the situation that lead to the dying of the various ghosts (a small battle, a brawl, a siege finally ending, etc). A few days later you come upon the exact same scene elsewhere - except they are not ghosts, they are still alive (and dying as you watch).
When the PCs arrive in town, they are greeted by name and with smiles by many of the townfolk. All the NPCs insist that the PCs once lived in the town, were well known and liked in the town, that since their leaving their (few) relatives have died, but their homes are still standing - if a little dusty and unkept. The longer the PCs stay in town, they more they 'recall' what the NPCs describe as their past - and they harder they find it to recall their actual past. If they stay long enough, they will no longer recall their actual past, having fully replaced it in their mind with the supposed past told to them by the NPCs. If they leave later seek their actual home town, they might discover that in fact their actual relatives have died since last they spoke with them - in the exact same manner as those in this town describe. Or perhaps the house(s) they show the PCs, insisting they belong to the PCs' families, are eerily similar to their actual homes in other towns, with details the NPCs could not have known about prior to the PCs' arrival.
When a creature dies, its shadow seems suddenly seems to come alive, pulling and straining to separate itself from the body. After a round or two it succeeds, rips away from the body, and slithers off into the nearest shadow, never to be see again. Alternatively, perhaps the soul literally leaves the body, bursting from it in a cloud of blood and viscera as it leaves to ascend to the sky.
Spells work as normal, but they have odd appearances. Entangle uses skeletal hands reaching out of the ground rather than plants, for example. Fireball appears like a burst of ectoplasmic slime that fades away after a round, after having caused the damage. Fog cloud appears to be a region where everything within it is actually inside a bubble of dark water - but can breathe as normal. Or perhaps when a spell caster casts a spell, a different one occurs instead - some have been 'switched' in their minds. If they ask others, the others saw the caster cast the spell that was actually cast, not the one the caster believed they had cast.
About to leave a town, you are advised that the next town is two days away - no matter what means of travel you use (walk, horse, boat, or even fly).
One day the PCs awaken to discover they have switched faces in the night. But no one they know seems to notice the change, or perhaps they act as if the switched faces were the ones they have been seeing all along.
A woman is seen crying black, oily tears. No one seems to find it odd except the PCs.
A valley appears to be normal - were it not filled with water. What appears to be a lake actually is a normal valley, with a forest, fields, a village, animals, people, etc. All are aware they are under water, but none think it is unusual, and nothing reacts as if it were underwater (no floating, no difficulty breathing, etc. Leading into the lake is a 'stream' of air ending at a 'pond' of air; fish swim and live in both. If the PCs try to enter the valley, they can only breathe normally within the air stream or 'pond'. They can leave such and speak while within the lake, and their words will sound as normal to the villagers, but as soon as the PCs try to breathe they will start to drown until they re-enter the stream / pond of air. Otherwise, everything is 'normal'.
Every time the party stops to speak to a common NPC, the NPC never looks in the face of the PC speaker; they always seem to look nervously just a little over the PC's shoulder; nothing unusual appears to be there, and when questioned the NPC usually has no idea they had not been looking into the face of the PC.
Creatures you are fleeing from always seem to be exactly the same distance behind your party - until you stop, then they slowly close the distance. If you run again, they remain at the new (closer) distance. You cannot escape this battle.
The PCs seem to be in a normal town, but if they look closely they notice that all the shadows of the people are moving differently from the ones casting the shadows. Yet whenever an NPC stops, somehow the shadows are exactly what one would expect for their position, lighting ect. Only when they are moving do the shadows move differently, even if the shadows always end up in the same position by the time the NPCs stop moving for whatever reason, even if suddenly and unexpected.
While speaking with an NPC, the PCs notice very small spiders crawling in and out of the NPC's mouth, nostrils, clothing, etc. The NPC notices and reacts to none of this, thinking the PCs delusional. Somehow, no matter how they try, the PCs are unable to catch any of the spiders for a closer look or to show the NPC, and if they have the NPC open his mouth, no spiders are visible.
Whenever the party decides to stop for the day and make camp, they find signs that a camp was recently made wherever they happen to decide to make camp. Eventually they realize the campsite they stay in each night is in fact the exact same place: if something is left behind or a nearby tree is marked, the same is found (or something similar but just a little different, a little off) is found in the ruins upon which the new site is setup, seemingly days old(er). If they try to stake the camp away from the discovered ruins of the former camp, they will awaken to find the camp set up in the ruins of the form camp - even if they post guards to keep watch for such, no guard will ever notice the change, and no sign of the encampment made away from the old repeating encampment will be found in the morning.
Strange reversals are witnessed. In the day one sees bats, while at night sparrows and crows fly about - somehow missing trees as they fly. When a fog comes upon an area, the PCs notice what appear to be fish and slimes swimming about in the fog as if it were water. If they look into a lake, they might see what appear to be trees and common animals walking about at the bottom.
For no apparent reason, animals start reacting strangely to the party members: growling at one certain member, cowering from another, and so forth. None act friendly.
The people in the town seem to speak - as if there is nothing strange about it - of the town having three sides. An arch in the center of town, depending which side one passes through, sends the travel to one of either of the other two sides of the town. All seem to exist in the same place at the same time, and in fact anyone entering the town from beyond its wall enters a different one of the three sides of the town depending on which town gate they pass through to enter it (one of the sides of the town has a south facing gate, another a north facing gate, another an east facing gate, a river borders the west of all three). Some buildings in the town seem to operate in a similar manner - existing in more than one of the sides of the town. Sometimes some of the people also seem to exist in multiple sides of the town simultaneously - perhaps without realizing it, perhaps realizing but not finding anything strange about it.
The same idea as the prior, but instead the arch is a vast mirror - showing a ruin of the buildings it reflects on one side and only wilderness on the other side. There are rumors that on certain nights (full moon? new moon?) the arch becomes a door into the past (wilderness side) or the future (ruin side).
The PCs pass a field being worked by NPCs. Upon a closer look, they realize the grains of the heads of wheat being harvested appear to be tiny maggot like insects. The NPCs find it odd that the PCs would expect anything else to be growing from the wheat, perhaps biting into and eatting a head off the wheat stalk (and the several grub-like 'things' that make up the 'grains') as the PCs are speaking to them.
One night, for no apparent reason, all the stars are blood red. Later, if the PCs ask whomever next they meet about the night, they discover that no one else witnessed the phenomenon.
If a cleric is in the party, one day when set upon by undead, he finds his attempts to turn them are in fact rebuking them. If he later speaks to other clerics of the same deity he finds only confusion: it has always been this way .... Or perhaps he learns that recently his deity has undergone a rather notable ... change, or has long been deceiving his clerics and followers as to his true nature.
Every now and then the GM sends a folded note to the player whose PC has the best perception check; the PC keeps seeing or hearing things - just to the side, or too small or far or faint to be noticed by most - that the other PCs do not notice. Are they real, or is the PC slowly going mad?
Every combat, at the start, the GM secretly rolls a d%; if he rolls under a certain number, all of the foes (or one foe, or all but one foe) are illusions. No matter how many are illusions, all vanish as if illusions upon being slain. If any are captured, they act confused and speak only gibberish (although without Tongues it may be difficult to realize they are not speaking an actual language unknown to any in the party).
All the creatures fought seem to have troll-like regeneration, but if torn open appear to actually be plant-like on the inside - despite their outsides looking like normal animals (wolves, bears, etc).
