An infamous example is the "Hot Coffee" (by which we mean sex) minigame from Grand Theft Auto: San Andreas. Apparently, some of the resources used in the Hot Coffee minigame actually were used in other parts of the game, which is why the data is on the final version of the game disc. It's also (most likely) thanks to Hot Coffee that the ESRB now asks game developers to see any dummied data when rating games.
San Andreas is also missing the interior for the San Fierro Police Department (which is why you respawn on a nondescript street corner near the building and you can't enter it, unlike the other ones,) presumably because entering it crashed the game or they didn't have time to clean up the programming for release, and hospital interiors as well. There is also text data for a skateboard hidden in the game's main files as well (which is why Los Santos has a skatepark.) The skateboard was scrapped for the presumably much easier to program and animate bicycles.
Don't forget the normally-inaccessible Andromada plane, tons of building interiors, and a substantial chunk of Liberty City.
The area of Liberty City where the opening of GTA 3 takes place is not seen anywhere in-game. Unless you can fly the Dodo, that is.
Text files in Grand Theft Auto V reveal that over half of the game's radio stations originally had much more content; in extreme cases, over half of the original playlist was cut in the final release. In addition, there are leftover files that suggest that Vinewood Boulevard Radio, an alternative rock station, was originally intended to be a 90's rock station called P.M.R, and that its conversion to VBR was a last-minute change (its icon for the station-select wheel is even still in the game's files!). Some of the cut songs were brought back in the enhanced versions for PlayStation 4, Xbox One & PC.
GTAIV has several vehicles that are inaccessible by normal means, which later appeared in the DLC episodes.
Bully, another Rockstar Games game, has a few as well:
Hattrick Manor. It's a house with a partially finished interior that can be entered with a well-timed bike jump. There's a mission where you have to steal a female student's diary back from Mr. Hattrick and it's believed that the original concept for the mission involved breaking into his house rather than the teacher's lounge at the school.
Several characters were dummied out. There were a pair of adults named Nate and Flynn, it's believed that they were for the cancelled Xbox version of Bully and would have been involved in uploading songs to the game.
A room that appears in the opening trailer doesn't actually appear in the game.
Bob, the wide-shouldered white kid in the mission cutscene for The Gym Is Burning, appears nowhere else in the game. The character model in his wrestling outfit can be hex-edited into the game, but a regular clothes model seen in old screenshots was removed from the code entirely.
There are a few cutscenes in trailers that were cut from the final version of the game, mostly likely to keep the T rating. One had Gary Smith pantomiming doggy-style sex, another was a closeup of Mandy's legs while she was wearing a towel.
Although skateboard and bike tricks weren't included in the final version of the game, there's a skate park that serves no purpose except for one mission, and lines of dialouge for watching someone screw up a trick in the data files.
The Boys' Dorm was originally intended to be a two-story building. If you stand far enough away from the dorm and zoom in with your camera, you can see the old two-story model.
Most of the new content for Scholarship Edition was dummied out of the original game, then readded.
The shop teacher Neil does not appear outside of his class, but strangely has dialogue recorded for roaming around like the other teachers meaning that he was removed. This might be because his dialogue refers to people he dislikes as "fascists".
Black & White has an Easter Egg where you move the mouse in a certain way and phoneboxes appear. Unfortunately, if you try to actually do anything with the Easter Egg, you get a message saying "sorry, the boss removed this cheat".
In The Godfather the map displays Barbers and Tailors as important locations but they are in fact just normal shops. They were meant to be where you would buy new clothes and change your hair but this idea got scrapped and instead you buy clothes and change your look outside the main game, when you select the file you wish to play.
These included an entire area called "Dark Valley Escape" South of Dark Valley (explaining the odd transition from Dark Valley to Cordon, where you walk through a gate and come out of a tunnel), a second mobile lab associated with the Americans and guarded by Freedom (see next point for a particularly obvious relic of this system), the swamp level that ended up in Clear Sky control bindings for cars and a helicopter, and a number of barely dummied-out weapons, equipment items (including useless anomaly detectors), and even several enemies. Early versions of the game also had mounted guns (the leaked Beta included a minigun).
Many players were puzzled by a glitch in one of the Yantar lab's missions, where Kruglov would wake after a blowout and become hostile to the player. This is because the Yantar lab is still Duty-affiliated, and the player's reputation can cause Kruglov to think they're an enemy.
The infamous "Chernobyl Dog" in Red Forest probably wasn't supposed to be in the game at all, given that it only appears once and the game crashes if you kill it. It's a strange Pseudodog with a Controller's screen-blurring attack and the ability to spawn clones of itself that attack normally but vanish if shot even once.
Red Forest also includes a strange door, likely to a missing area; a combination lock leads to a small room with another door and nothing much inside.
Several NPCs carry useless items; it's possible to get hold of a guitar, a harmonica and a pair of goggles called "hand_radio."
The original game's artifact descriptions name one called "shell" that never actually appears. Descriptions of cut anomalies called "lift" and "time" are present in the game files; respectively supposed to create the artifacts Pellicle and Mama's Beads.
In the Spider-Man 2 game, jump from boat to boat until you get to one that's farthest southeast from Manhattan. Now take a fully-charged leap as far as possible into the sea further southeast. Right before you hit the water and get teleported back to shore, you'll see the words "Governors Island" show up as if you were entering a new area, but there's nothing but water there. This indicates that Governors Island was going to be visitable but it was cut.
Saints Row: The Third had several plot threads, alternate endings and story ideas scrapped during development, which explains why the game feels a bit rushed story-wise. You can read the details here.
Minecraft had several items that were present in the game during alpha and beta and it took years for most of the items to have any purpose. The most well known dummied out item is the quiver, which probably would have allowed the player to hold more arrows than normal, but even to this day, the item is never used and still exists in the game's files... only to pop up again in development screenshots for release 1.9's "Combat Update", finally averting this trope.
The Ender Dragon and the Wither were implemented into the game before they had any purpose. The Ender Dragon appeared in the 1.9 beta, but it could not be spawned at all unless you used a mod to do it for you. Likewise, the Wither was planned for version 1.4 and was going to be in one of the test versions for players to try out, but the developers had to dummy out the mob since spawning him would crash the game. The next test version of version 1.4 rectified it.
The game also had several status effects implemented once potions were introduced, but many of them went unused and buried in the game's code. Several of the unused effects were eventually put back into place, but a few others still remain dummied out without mods.
The Giant, which is basically a gigantic Zombie, can only spawn when the light level is more than 11 AND less than 8. Obviously, this is impossible. If spawned in through other means, it basically just stands there.
A handful of excised sprites exist in the files for Yume Nikki. They include such things as Madotsuki's window but with cracked glass, another window with the reflection of the city on it, and an older model for the "Triangle Kerchief" effect. There are also some huge inaccessible islands in the east part of the Famicom World.
Terraria has a number of items and weapons that are dummied out for various reasons.
From the early development days is a Zapper gun that was meant for the developers to defend themselves effortlessly while testing things.
The S.D.M.G machine gun is currently not accessible without cheating it into your inventory. The same applies for the Gravity Globe, which functions like an infinite Gravity Potion.
Several items in the post 1.2 era were occasionally bugged and unable to drop or spawn until subsequent quick-fix patches corrected this.
A couple of weapons were never implemented due to worries about copyright, such as a scythe modelled after a weapon in Soul Eater and an ice sword which was a more blatant copy of Frostmourne from the Warcraft franchise.
As of version 1.3, the S.D.M.G, Gravity Globe, and developer items are all available. The first two are drops from the new Final BossMoon Lord, and the developer items can be obtained from any Hardmode boss's Treasure Bag that drops when beaten in an Expert mode world. As such the developer items no longer give debuffs when worn, instead serving as cosmetic wearables, with most developers also having a unique set of wings (Red's Wings no longer have infinite flight time) and a couple having Yoyos as well.
Watch_Dogs got a fair bit of griping on release for having graphical effects in the E3 demo that turned out to not be in the actual game. Shortly afterward, it turned out that those effects were still there (at least, on the PC version), they'd just been turned off for no obvious reason (they didn't slow down the game or anything). One of the most common mods for the game is one that turns them back on.