Hollows in Bleach could not be seen by anyone who could not see dead people. This lead to the first few episodes having these...things chasing people that nobody could see. Only the footprints and scenery destruction following them.
Even those who can see dead people have trouble seeing them; you need to have a lot of dead person energy built up. Even Ichigo couldn't see them until the start of the series, and he had trouble telling the dead from the living when he was younger.
Not seen (but present) in the live-action film The Blade Master, since visible monsters would've strained the budget.
The film Captain Sinbad has the title character face an invisible monster that leaves dinosaur-like tracks in the ground (that form from an explosion as its feet land). Considering all of the Special Effects Failure monsters that appear, it's rather startling.
Parodied in Red Dwarf, with a B movie titled 'Attack of the Giant, Savage, Completely Invisible Aliens'', which consists of Bad Bad Actors pointing at the sky and saying "It's the giant, savage, completely invisible aliens!"
An Episode of The X-Files featured the angry spirits of animals being abused by a circus manifesting as physical, but invisible, phantasms: one fellow got mauled to death by an invisible tiger, on-camera, both out- and in- universe.
The Krafayis from the Doctor Who episode "Vincent and the Doctor", although it shows up in mirrors.
Played with during The Face of Evil. When some of these start chasing the Doctor and Leela, the Doctor deduces that the creatures can't be following them by sight, since light would just pass through their eyes if they even had them. He uses the vibrations of an alarm clock to distract them.
In "Midnight", the monster was more or less invisible, only 'showing' itself when it inhabited other people's bodies. We never did find out what it looked like.
The Visians of planet Mira in "The Daleks' Master Plan" are this played straight.
Stargate SG-1 has featured the Re'tu, big spider aliens which are invisible because they are "180 degrees out of phase from normal space-time".
Batman had such an episode in its cheap 3rd season and it took the concept even further in the climatic fight when the heroes kill the lights to even the odds fighting against multiple invisible enemies and the fight concludes in total darkness.
Dungeons & Dragons has several invisible monsters, but perhaps the invisible monster is the Invisible Stalker ("pictured" above), which is, well. The 2nd edition Monstrous Manual features an illustration for every monster entry, and no less than two people are credited for the illustration for the Invisible Stalker... which is, of course, a blank.
Also Hellcats, also known as Bezekiras. They're lionlike feline monsters from Hell that are invisible in the light, but appear as a glowing silhouette in darkness.
In Amnesia The Dark Descent, one of the most frightening areas is a basement flooded knee-deep with dark water. Shortly after entering the water, there is a splashing sound in the darkness ahead and then you only hear and see the splashing footsteps of something charging right at you. As long as you keep climbing on the crates that are littered through the area, you are quite safe, but as soon as you step into the water or drop something into it, the invisible creature comes charging again.
In a later section, you enter a mostly drained cistern which has walkways that lie above the water. Many players never enter the water at all out of fear that there could be another of those creature in it. There normally isn't, but when you take too long in the room, the game adds one, even if you have stepped into the water safely before.
Let's not forget Ganon in the original game. He's invisible until you can shoot him with the Silver Arrows, except for a very brief period after you strike him with your sword. The only way to figure out where he is is by extrapolating from the start location of the fireballs he shoots.
There are a number of enemies in the Metroid Prime games that require the use of other visors to track. You usually run into at least one before you get the visor...
That robot guarding the Power Bombs in Metroid Prime is an exception as it is invisible to all of the available visors, but its stealth is ruined by muzzle flash.
It also can't be scanned or locked onto. However, if you have the Wavebuster, prepare for a short fight (thank god).
The Chozo Ghosts, which are invisible when not attacking. You need to use the X-Ray visor to see them.
The Omega Pirate makes itself invisible when it's recharging. You need to use the X-Ray visor to see it. But just in case you weren't paying attention to the boss's recharging health bar, visible Beam Troopers show up as a distraction...
The second form of the Metroid Prime itself occasionally makes itself invisible to the visor you're using.
Corruption has the Steamlord miniboss, who is invisible most of the time until he has to revive his flunkies. It's possible to fight the last one of those after getting the X-Ray Visor, which makes the fight a lot shorter.
Unfortunately however, enemies using hypermode short out that visor, making those fights very annoying on the highest difficulty (where any enemy that can go into hypermode most likely will do so immediately)
The Assassin in Dark Messiah (multiplayer). 'Can' attack when invisible (breaking the invisiblity), however, the invisibility itself is more of a cloak meant to assist in stealth - walking in bright-lit open areas around sharp-eyed players will get the Assassin spotted.
Perfect Dark has a weapon that gives the mooks a cloaking device.
The Jedi Knight games have the Force Power "Mind Trick" which in multiplayer renders the players invisible.
Super Smash Bros. Melee also has the cloaking device. As a few comic strips have noted, in Smash, if they can't see you, you can't see you either. This generally results in such mishaps as falling off the edge of the map. But to be fair, when you move or attack, you have a Invisibility Flicker, so you aren't blind.
On the positive side, the user accumulates no damage for the duration. For some reason.
And, of course, there's the bonus for pulling off at least one KO while cloaked.
The Sorcerers in Gauntlet, distinguished by their purple robes, wink in and out of existence as they charge towards you. The Super Sorcerers in Gauntlet II are able to use this ability tactically, appearing at the edge of the screen, firing at you, and then disappearing.
In FAMOUS has some enemies in the third island that can cloak themselves - the flying grenadier machines, and the shotgun conduits.
Bitterflies in Castlevania: Symphony of the Night, which phase in and out of visibility in large, seemingly empty rooms.
Strangely avoided in the sequel Portrait of Ruin, where there is an Invisible Man enemy, but they actually start out wearing a hat and trenchcoat, so you know where they are. Once they sense you, however, they take off said hat and trenchcoat and really are invisible (barely visible via a few intentionally misplaced pixels here and there). However, it's rare that they'll be able to do much while truly invisible; they don't take that many hits to destroy.
Both of the above enemies are back in Order of Ecclesia.
Nemesis and Alastor in Aria of Sorrow are invisible enemies with visible weapons. Nemesis's soul grants Soma the ability to turn invisible. There's also the Sky Fish, which isn't invisible— it's that weird shooting star thing you see in certain rooms. Betcha didn't know THAT was a monster!
The GameCube remake of Resident Evil features a challenge mode in which all of the monsters are invisible. Prepare to die repeatedly.
Resident Evil Revelations features the Farfarello enemies which are invisible versions of the Hunter enemies from previous games. Now, consider that the Hunters were already Demonic Spiderswithout being invisible, and that Farfarellos only attack in groups...yeah, you better pray that you don't get swarmed by them and caught in a hit/stun lock, and that you have enough ammo left over, because you're probably gonna die otherwise, even with them being weakened somewhat compared to the Hunters from previous games.
There is a type of invisible robo-coptor in Mega Man ZX Advent. Sirnaq's/Model P's radar can see them though, and shoot them. They also do an Invisibility Flicker when they shoot.
There is a variation of this in World Of Warcraft. If you visit the Kodo Graveyard, there are visible vultures that are hostile and will attack you, but if you visit the graveyard while dead in spirit form, you will notice friendly Kodo Spirits scattered around.
There are also level 50 invisible ghosts in one area of Duskwood. A zone for characters at about half that level. Prepare to die if you hit one by accident.
In the same vain there are level 5 ghosts in the courtyard outside of Undercity. These are much less a threat as by the time you hit the zone you're already level 5 and you don't have any spells that would hit them at this level anyways. Both of these can be seen with spells or potions that detect invisibility.
Interestingly, both spirit form and invisibility follow a pattern where if two entities have it, they can still see eachother. In some dungeons, the Mage's Invisibility spell was useful to spot monsters who were invisible for that exact reason.
Nethack takes this to the extreme. In addition to having two types of enemies that are permanently invisible, it contains methods that allow pretty much any creature in the game to become invisible.
Potions/wands of invisibility make living things (not items) permanently invisible. If a monster sees one on the ground, it will pick it up and use it. To top it off, these are considered "defensive items" and pretty much every monster has a chance to receive one at spawn time.
Cloaks of invisibility. Monsters that can wear armor will pick them up and don them.
Every sufficiently high-level spellcasting monster can cast an invisibility spell on themselves. Every sufficiently high-level spellcasting monster usually does the moment they see you.
In Final Fantasy VII , if you hit the 'ghost' monster, it turned invisible. You could still target it, but you would almost certainly miss. Not so in reverse.
Final Fantasy VI has an invisible Bonus Boss on a small island. It is Lost Forever when the world explodes. Enemies also become invisible when they have the Vanish status effect, although they can still be targeted. This doesn't happen when your characters have the effect.
Final Fantasy XII has a baker's dozen or so of monsters who like to shake things up by being invisible.
The Halo series has invisible enemies and a Power-Up that can turn the PC invisible for a period of time.
The weapons are still visible. One of the funnier moments in the original was watching Too Dumb to Live elites charge you invisibly with massive glowing energy swords fully visible in their hand, completely negating the point of the invisibility. They'd have been better off going with the old-fashioned blue armour, the light blue shieldless armour of the invisible elites is the lightest armour in the original Halo and allows the bearer to be taken out with a single headshot as easily as a grunt. This recieved much mocking in several flash videos.
Mega Man Legends has rather nasty variant in one specific dungeon; Sharukurusus, normally, are fast-moving, hard-hitting robots that chase you down relentlessly upon sighting you and attack with a nasty spinning drill-claw attack. Now imagine taking that and giving it a cloaking device so you can only see it JUST BEFORE IT SLAMS INTO YOU. What makes it worse is that you can still hear their footsteps, so you can hear them charging at you beforehand, but won't know where they'll be attacking from until they're right on your ass. Thankfully, though, you don't have to fight them and can easily avoid them by staying on the higher ledges of the room they're in.
Unless you're going for the chests, in which case one Reaverbot will ambush you just as you exit the alcove.
Cosmos Cosmic Adventure, one of Apogee's old games, had invisible robots that would shove you backwards if you bumped into them. You could barely make out their outline, and if you jumped on them enough, they would become visible. Walking through them from behind would also hurt you.
Two versions exists in La Mulana : One that moves so fast that you have to stop time to see it, and one that merely requires that you get an item to see them... after going through roughly 10 screens taking random hits from them.
The boss of Chapter 3 in Super Paper Mario is a nerdy chameleon who turns invisible and invincible and runs around the room. However, he has to drop his invisibility to attack you.
In Rogue, there are the Phantoms, which can only be seen if you're wearing a 'see invisible' ring.
Baldur's Gate loves this trope. Most wizards will use some variant of Invisibility (usually Mislead) thieves love stocking up on Potions of Invisibility (especially nasty are the "Rune Assassins" featured in one quest, that have a very nasty backstab and a near-unlimited amount of potions...) Throne of Bhaal ups the ante further, introducing a dragon that turns invisible, and who cannot be detected unless you use a particular sequence of spells. Ouch.
Kirby Super Star had Chameleo Arm, which tended to be invisible...and tended to fire balls of paint which the protagonist could get the Paint ability from to reveal and damage him with.
StarCraft's Dark Templar are invisible, and capable of hacking your average infantry unit into two hunks.
Invisibility is a somewhat important unit attribute, in fact, as stealth units cannot be directly targeted for attack. When fighting a Terran or Protoss player one should always have detector units handy or else be left helpless. Zerg units can't move while invisible but they can burrow to set up ambushes.
Dawn of War games use a similar system to the aforementioned Dark Templars to represent infiltrated units. In the classic and Winter Assault expansion, this was generally limited by disabling the unit's ability to attack. That is, until Dark Crusade, which enabled attacking while infiltrated without revealing the unit. This was balanced by different races' detecting units and abilities, but it didn't diminish the cheapness of using massed infiltrators.
Dawn of War II fixed this by making infiltrators reveal themselves if they attack, or if they get within arm's reach of any enemy unit. This is with the exception of the super-infiltrated Cyrus, who can use his incredibly destructive array of explosives and specialist ammunition without breaking Infiltration, but will be otherwise be revealed just like any other infiltrated unit.
If you eat the corpse of an invisible stalker, there's a chance that YOU can become intrinsically invisible.
Like NetHack it also has spellcasting monsters who will turn themselves invisible.
EverQuest 1 used invisible monsters primarily as Underground Monkeys. Among the more notable in the early days were the Enchanter pets and the shadowed men. In both cases the characters were invisible but the weapons they carried were not.
Kingdom Hearts gives us the Stealth Sneak, first as a Boss Battle, then reappearing later on in the Hades Cup. The icing on the cake is one of the latter seeds, consisting of not one but two Stealth Sneaks to carve up. Mind you, locking onto and hitting one is not affected by whether they are visible or not. They can be detected by sight alone if you look very carefully. Their camouflage produces a "heat ripple" effect, though this is easier to see during the boss fight than during the seed match.
Birth by Sleep also gives us the boss from the Secret Episode. For the entire first part of the fight, the only parts of it you can see are its glowing red eyes and, when it attacks you, its claws.
Silent Hill Origins has invisible monsters in Cedar Grove Sanitarium. The only way to tell where they are is by the metal harness floating in midair, and the eerie person-shaped shadow they somehow cast. Oh, and by killing you in the dark.
Silent Hill 2 has a single invisible demon in Toluca Prison. However, since it's trapped in a cell you can't open and can only be "seen" by James jerking his gun toward it when you're close enough, a lot of players fly straight by it without even noticing the first couple of playthroughs. It can be heard, saying something that could be anything from "ritual" backwards to "I buried Paul", but strange noises are so commonplace in Silent Hill that you don't make that link until you kill it and hear the absence of the sound.
The original game has Larval Stalkers, which can't actually hurt you, and later, Shadow Children.
There are invisible monsters (that look kind of like a cross between a red cartoon pig and one of the demons from the same game series) in Catacomb Apocalypse. Unfortunately the creators of the game seem to have been rather intimidated by the thought of turning the awesome power of invisibility against the player, so the monsters blink into visibility all the time, move fairly slowly and can't take that much damage, and don't shoot, making them if anything easier than normal opponents.
Diablo has the genuinely creepy The Unseen, which do come visible when they attack, but before that could fill the entire room without you knowing it.
Due to a bug in the level generation routine, they do not respect the safe zone around the entrance. So when you just arrived in the level and you are gathering your bearings, casting Mana Shield, checking item durability, etc., they could be right behind you, getting closer. And if this is multiplayer mode, your gear is now on the floor next to a sea of enemies right at the stairs.
Chapter 10 of Eternal Darkness features a telekinetically vampiric creature who turns invisible when he's not attacking anyone or getting healed at a shrine. Mercifully, you can use a spell to reveal him.
That spell is less useful in the final chapter, when it can reveal only some of the invisible Trappers in a room. Good thing they can be Helpful Mooks.
Plants Vs Zombies has the mini-game "Invisi-Ghoul". ALL The zombies are invisible. The only TWO ways to detect them is to 1. use an ice-shroom to cause ice to appear around their feet or 2. the audio cues they make when they appear. Oh, and the Zomboni that runs over your plants in one shot? Yep, it's fought in this minigame.
Do-it-yourself variation can be (not) seen in Daggerfall. This game allows players to create their own spells - so it is possible to create custom-made Invisibility spell for casting not on yourself, but on your opponent. Thus player can make opposing monsters invisible - complete with tell-tale blood flying when they are hit.
In Shin Megami Tensei Strange Journeyevery monster is invisible. Fortunately you soon get a program downloaded into your power suit that allows you to detect, confront, and communicate with the demons. However, until you've killed them at least once, every non-boss monster will be rendered as a blob of static that you can't analyze.
The Fallout 3 addon "Operation Anchorage" includes Chinese snipers, who start off cloaked as though using a Stealth Boy power-up. Until they become visible, the player can't target them with the auto-aiming Vault-tec Assisted Targeting System.
Nightkin in Fallout New Vegas have the same effect, which much more difficult to see at night while climbing Black Mountain. Even worse are a pack of Nightstalkers, mutant coyote-rattlesnake hybrids, that can also cloak. It's nearly impossible to make out the tell-tale visual distortion in their dark cave, especially since they're so small and quick, but you can hear their faint rattling and hissing as they approach, sometimes in packs.
The turn-based RPG Odium features, near the end of the game, a group of invisible monsters which are visible only when they move. You have to remember where they stopped so that you can shoot them (explosive weapons come in handy, as they cover a wide radius). Or you can just look at your character's movement range and check which squares are mysteriously inaccessible...
Anything that has stealth in The Lord of the Rings Online will appear invisible until the player is nearby and facing it. By then it may already be too late, especially if the player is a ranged class.
In Mario Adventure, ghosts are invisible when you are looking at them. Thankfully they still don't move during this time.
One of the most frustrating missions in Jak II involve slaying 30 invisible Metal Heads in Haven Forest. They come in two flavours: humanoids with guns instead of hands which shoot at you from afar and keep moving all the time and big, bulky crabs with machine guns that drop their camouflage when they first spot and procceed to blast you away. The first kind make a brief return in Jak III, although only in one quest.
One level of Pathways Into Darkness is populated by Wraiths, who can only be seen with infra-red goggles. To trip you up, there's also a Banshee in the level, who can't be seen while you have the goggles equipped.
In Wizard Of Wor, Garwors and Thorwors could turn invisible at times, though they would still appear on the radar screen.
Certain enemies in Bubble Tanks 3 have the ability to use stealth, which turns them invisible. Bubble Tanks Tower Defence has the Stealth enemy, which is invisible to the player. When damaged, their invisibility wears off for a short time.
Mini Robot Wars: The Mole is able to dig underground unseen, while the Ghost is able to fly past your units unseen. While the player can see them, the minirobots will not unless you have a radar or surveillance robot platform.
Nintendo Land has the Luigi's Ghost Mansion multiplayer game, which is an interesting inversion where one player actually gets to play as the invisible monster. The person playing as the ghost uses the game pad and is invisible to the other players, who are trying to shine their flashlights on him.
Dungeon Crawl: Similar to fellow Roguelike Nethack above, Crawl features permanently invisible monsters as well as an Invisibility spell and wand that will be liberally employed by any monster with access to them. Because enemies you can't see get considerable bonuses in combat and can easily corner you without warning, finding some means of seeing invisible is a high priority for any player that wants to survive beyond the first few levels.
Cor's tickle monsters are invisible and amorphous. They wear gloves when they want to be seen. Lots and lots of gloves.
One Jonny Quest episode is titled "The Invisible Monster". At least, it's invisible until the heroes cover it with paint, allowing them to see it—and then destroy it.