Silent Hill 1 has several dummied-out rooms in Midwich Elementary School. Also, the Bottomless Pits were intended to be death traps as in the later games, but you can't fall into them during normal gameplay.
The boat was meant to be a vehicle to reach the lighthouse, as evidenced by Harry looking at the steering wheel although it does nothing. There's also a car engine at the gas station that serves no purpose.
Silent Hill: Homecoming has a ton of unused voice files that hint at various dropped characters, a cameo by Walter Sullivan of Silent Hill 4, a larger amount of involvement by Deputy Wheeler, and lots of explicit backstory before it was made more subtle. There's a blog entry going into tremendous detail, here, as well as a YouTube video containing some of the unused dialog here.
A truly horrible example of this afflicts a certain version of Resident Evil 3: Nemesis. This is somewhat odd in that it is only a particular re-release of the game, not the release for a certain country or console. Players of the original Playstation version found that completing the game would get them a "boutique key" item, allowing access to the secret costumes, and would also unlock "The Mercenaries", the extra game mode in which you unlock weapons for use in the main game. The Dreamcast version of the game was a little strange. There was no boutique key, and indeed the Boutique is inaccessible. Instead the player has every costume when they start the game. The Mercenaries still functioned as normal. The PC version is a port of the Dreamcast version, the same in every way but one. "The Mercenaries" is accessible from an entirely separate .exe file instead of from the main menu of the game.
This incident occurred when a certain company known as Xplosiv (they specialise in releasing cheap versions of old PC games) brought out their version of Resident Evil 3. "The Mercenaries" mode was completely and utterly missing. They'd even deleted the pages about it from the .pdf file instruction manual, but had left in the contents page which clearly said it should be there. The Mercenaries mode can be replaced by downloading its .exe file, if you can find it online. But it still won't make the game fully playable as originally intended by Capcom. Why? Because the Xplosiv release also removed the function allowing you to save your completed game file. Weapons unlocked in "The Mercenaries" can only be used in a second play through a completed file. As a result, Xplosiv have managed to break every single unlockable item in the game, remove most of the replay value, and caused many many fans of the game to scream in frustration and horror as they realise what has happened. WHYYY!?
Resident Evil Outbreak and Outbreak File #2 both contain data for extra character costumes not normally acquirable in the games, and it's largely speculated that these were intended for a File #3 if it ever saw the light of day. A Game Shark can be used to put them in the game proper, but while the games were online, Capcom eventually locked out accounts that were found to be using these inaccessible characters.
The PAL version of File #1 had the online multiplayer completely disabled. In a game whose entire gimmick was that it was an online multiplayer survival horror.
Poking around on the Resident Evil 2 disc with a Game Shark reveals a number of items and weapons that were cut from the final game, including a machine gun called the Calico.
Several areas and one complete subplot were cut from the original release of Resident Evil. George Trevor's diaries were completely cut out and only evidence of the scrapped graveyard area is a split-second view of its entrance in one cutscene. Both were restored for the 2002 remake.
Very early in development they also intended to have cryptic messages written in blood on the walls, left behind by the infected people in the mansion as they lost their sanity. They were actually removed from the DualShock version, but the original hid them by simply recoloring them to match the walls. By tweaking the game color palettes with an emulator, you can see them. This one reads "For God's sake GET OUT!!!"◊
There were also "Dum Dum" rounds for the magnum. They are fully functional in the game, being slightly more powerful than magnum rounds, but without a Game Shark the only evidence to their existence is the phrase "it is loaded with Magnum rounds" in the description of the colt python which implies there is more than one kind of ammo (Like with the bazooka). Oddly the 2002 remake has the same rounds again dummied out, and the same description for the magnum!