Early in the game it's possible to sell your equipment to buy an Escapipe, an item that allows you to leave a dungeon. You're thrown into a dungeon by your father, and it's possible to then use the Escapipe to leave. This will lead to a unique conversation where your father tells you that while normally such a tactic is a clever idea, you have broken the game and must restart.
Playing the Corrigan Aus. stage during the night and driving down a blocked off road will result in your car's electrics cutting out, followed by a UFO flying over and abducting you. Once you return to the track, your car will be made of jelly.
Watching TV at 4:44 AM or PM will cause the number 4 to appear repeatedly on screen along with a Japanese riddle-like text. This was most likely put in to freak out Japanese gamers, as four is sometimes pronounced "shi" in Japanese, which is also their word for death.
There are two statues that appear at the end of the game. If you strike them, nothing happens to tell you they are of any significance. But if you keep hitting them (200-400 times) they will finally break. A scrambled code will show on screen. Decoding it reveals a 1-800 number. Calling the number will put you through to a recorded conversation between Kratos and David Jaffe, the game's director. Kratos eventually gets fed with David and kills him, ending the call.
In the original release, Batman and Spiderman appear as bosses. Batman was later replaced by a different enemy, while SEGA added a copyright disclaimer for Marvel Comics, who allowed Spiderman to stay in the game.
In Donkey Kong's cabin hangs a picture of a dolphin. This is a reference to the code name of the Nintendo Gamecube, "Dolphin". The game was released before the Nintendo Gamecube was revealed, and is thought to be the earliest reference to the code name "Dolphin."
On the planet Noveria, when the player attempts to restore power to the Peak 15 facility, the virtual intelligence "Mira" immediately appears and says "It looks like you're trying to restore this facility. Would you like help?" This is a nod to Clippit, the infamous Microsoft Word paper clip helper character, who was infamous for popping up and offering unneeded and unnecessary help. Shephard's Renegade response is "Oh crap, a pop-up."
After beating the game you have the option to replay using everything you acquired through your first play through. Using this to beat the game's main villain at the very beginning of the game will unlock a secret ending where you meet the game's developers at the End of Time.
If you enter Konami's official customer support phone number into your phone, you will be pushed through to an operator who acknowledges that you are calling from Silent Hill, and that you are beyond even their help.
There's a fossilized dog called Seymour in the Lonesome Road DLC. Seymour has the appearance of a normal dog, but at a reduced size. His inclusion in the game is a reference to the Futurama episode "Jurassic Bark" in which Fry finds his dog Seymour fossilized and tries to clone him.
In the NES version of Bomberman, if players complete the 50th level it'll reveal Bomberman's true identity to be Lode Runner. Bombermen also appear as the enemy robots in the NES port of Lode Runner which was developed by Hudson Soft.
There is a secret room, called the Chris Houlihan room, that is not accessible via normal means. It contains a telepathy tile and 225 Rupees and is used as an error handler if you fall into a hole but the game can't find a proper destination.
This room appeared as a result of Chris Houlihan winning a Nintendo Power contest and being promised an appearance in a Zelda game. Many of the glitches used to access the room were removed in the GBA port though, along with any mention of Chris.
Chun-Li, from the Street Fighter series, makes a cameo appearance in the game. In Bleak, speak to the magician who says that he can make 100g disappear. Answer "yes" twice, "no" twice, and then yes. You'll see Chun-Li in a small room performing her famous Lightning Kick.