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SCPs
SCP 472 The Bloodstone
Ingame mechanics: You can find it in its containment room. If you stay in its presence for too long or if you pick it up and take it with you, it will cause you to hallucinate blood on the walls, a loud heartbeat, and dead bodies, some of which move around and and others may appear suddenly when you blink, behaving similar to hostile SCPs but won't actually hurt you. It will also change the appearance of hostile SCPs to look similar to the halucinated bodies, making it difficult to tell what is real and what isn't. The advantage to doing this is that Hostile SCPs are also affected by it and may become confused when in your presence while you are carrying it. It will also drain your health and sanity, but at a rate that is so slow that it isn't really noticeable, but still enough to kill you if you don't pay attention.

SCP 479 Hallway 4, D-Class Dorms, Site 14
Ingame mechanics: This is just an atmospheric effect. Some of the hallways will have blood appearing on the floor in front of you with a sound similar to dripping or splashing water.

SCP 178 "3-D" Specs
Ingame mechanics: If you put these on you will see strange creatures. They attack you if you touch them, although they are easy to avoid because they usually move away from you if you get too close, although there is a small possibility that one will decide to follow you. If one does follow you, you can stop them by closing a door behind you. A possible use for this item is that you can refine it in SCP-914 to turn into something more useful.
(A mod has been created that as this SCP to the game but I didn't think it was done well enough.)

SCP 1404 Cereal Bowl
Ingame mechanic: mostly the same as its article. it will exist in the game just to creep you out. I think it would be best if you found it in an unexpected place.

SCP 1090 Cordless Headphones
Ingame mechanics: make you hear unsettling music and sounds. if you wear it for too long the music will continue even after it is removing it.

SCP 627 Perpetual Circle
Ingame mechanics: Found in is containment room, surrounded by a lot of equipment, but does not do anything other than look unsettling.

SCP-572 Katana of Apparent Invincibility.
Ingame Mechanics: Causes you to die stupidly if you obtain it. If you pick it up, you will receive a message saying, "Katana of Apparent Invincibility Obtained: Victory is Certain, Nothing Can Stop You Now, You Win!" The game's music will change to an epic song, such as "Indestructible" by Disturbed, which fits because this is how SCP-572 makes its holder feel. SCP-173 will spawn at the entrance to the room and your character will automatically attempt to attack it with SCP-572, only to get killed by it. In your dying moments the music changes back to normal and you receive the message, "I lied"

SCP-002 The "Living" Room
Ingame mechanics: You can find it inside of a large room, which has more than one exit, so you can pass through it to reach other rooms. While you are inside of the room containing SCP-002 it is possible to enter SCP-002 and look around inside of it. While you are inside the room containing 002 your sanity meter will drain, but at a very slow rate, and so you actually can stay in it for several minutes safely.

SCP 017 Shadow Person
Ingame mechanic: The same as it's article, although it might be difficult because it uses shadows and I am not sure if the game would support something like that. It might possibly be used as a way of trapping other SCPs.

SCP 650 Startling Statue
Ingame mechanic: same as its article. Unexpectedly appearing behind you when you turn around and causing you to jump backwards in fear.

SCP 743 A Chocolate Fountain
Ingame mechanics: Heals the player and boosts stamina if they drink from it but this will increase the probability that it will attempt to hunt them down.

SCP 718 Eyeball
Ingame mechanics: Works very similarly to its article. A large group of them is found in a heavily secured room, attached to the walls, floor and ceiling, plus a few that are mobile. If look at them for too long, you will be drawn towards them and will attack them, causing them to explode and replicate. You can use them for trapping 173, although this is very risky. When you cause 718 to explode it is possible that new ones with form on your body, which can be helpful to you because it will improve your vision and make you incapable of blinking. The cost of this is that you are much more vulnerable to sanity damage and if you reach the end of the game with 718 on your body it will cause a bad ending.

SCP-1129 Hyperarousal Response
Ingame Mechanincs: I am not entirely sure if this one would work but it is a good idea. Read the article. If you don't want to read article, basically it is a bizzare looking creature that causes extreme fear in anybody who sees it and may cause permanent paralysis if you see it too many times. In the game, if you encounter it, you would have to avoid looking at it to get around it. If it is added it might have to work somewhat differently than the article says.

SCP-956 The Child Breaker
In game Mechanics: it somehow got loose during the massive containment breach due to the fact that it was being tested on when the attack occurred. It wanders around the facility and can be randomly encountered similarly to 173 although much less frequently. It is possible but unlikely to see it moving on the security cameras. While you are in the same room as it, or in any adjacent room as it when the door is open, it will not move. It is able to open doors but it will not open any door leading to the room you are in if it is in an adjacent room the way 173 will. It is possible to discover the room where it was contained along with it's SCP document. Near the end of the game you may hear that the MTFs have contained it, or that it has escaped from the facility.

SCP 796 River Cat
In game mechanics: When you start a new game there is a small probability of this thing stalking you throughout the game. You can see it when you are in dark areas, usually following a short distance behind you, sometimes making soft footstep sounds.
(I think that this one is already in OnyxDarkKnight's list at the beginning of this thread)

SCP-882 A Machine
Ingame Mechanics: The room containing SCP 882 is a safe zone that 173 can't get into as long as you keep the doors shut although 106 can get in. This is because nothing in the room containing 882 contains anything made of metal, this includes the doors leading to the room. You stop 173 from getting in by sealing the doors from the inside once you enter. The room may contain a needed item such as a key card. Staying in the room for too long will cause you to hear a metal grinding sound that gets worse over time. This sound will very slowly disappear after you leave the room. 882 itself is suspended in a massive tank in the floor the room. Jumping into the tank will cause death. You will be forced to do this if the grinding sound gets too loud.

Joke Items
SCP 001-J The Big Red Button
Ingame mechanics: Causes the game to immediately crash if you push it. I think it will work best if it shows up somewhere that seems out of place. It might or might not have a "do not push" sign. Either that or you should be able to find it at the end long and heavily secured hallway that is difficult to unlock to and takes several minutes to reach the end of.

SCP 006-J WHAT THE ____ IS THAT THING
Ingame mechanics: You can find them in containment and also you might see them crawling on the walls or floor.

SCP 014-J A Fork
Ingame mechanics: It is heavily contained although it does not appear to do anything. Although if you have it in your possession at the end of the game it causes a silly alternate ending.

SCP 536-J It's On The Back Of Your Head.
Ingame mechanics: You can find a document similar to this one. If you read this document it and then make a sudden move it will kill you.

SCP 2558-J Pufferkittens
Ingame Mechanics: You can find one of them wandering around. It will act cute and will puff up when dangerous SCPs are nearby.

Other Suggestions
I have some suggestions for some possible events involving SCP-035. SCP-035 has a lot of potential as a character and so I hope to see a lot more possible ways he could be involved with the story.
I think that it should be possible for SCP-035 to have interactions with other SCPs. An excellent idea would be for SCP-035 to take possesion of SCP-173 or SCP-106. It has been noted in the Article for SCP-035 that it is able to posses not only humans but also humanoid objects. Here is how an interaction between 173 and 035 would go. If 173 and 035 encounter each other 035 will stare at 173 for several minutes and will speak to it in a strange language before 173 kills 035's current host and puts it on. This is good for the player because 173 will no longer be aggressive to the player while possessed by 035. However, doing this will have consequences later in the game. Most likely what will happen is resulting in an alternate bad ending where SCP-035 helps the player escape only to betray you in the end. Similarly it also is possible for SCP-035 to encounter 106. 106 will attack 035 and they will both disappear only for 106 to later appear possessed by 035. If this occurs the ending is even worse than what happens when 035 possess 173. 035/106 will escape from the facility with you, managing to avoid the trap than normally stops 106 and you will be caught by it and tormented by it for a much longer period of time than that what 106 normally puts you through before eventually 106's body gets too weak to continue and 035 takes your body as it's new host.
I also would like to suggest that some conversations between 035 and 079 be possible to occur.

Another idea I have is that there should be an option to adjust how many and how often Joke items and silly events will be encountered. If a whole lot of joke items and silly events get added to the game i think it would make sense for players to be able to make adjustments to how often they show up so they won't be distracting.

I think that the room where SCP-008 is store should have its appearance changed to look more like what a room for storing Biohazardous materials would actually look like. And I think it would be good if it were also possible to find other SCP diseases along with it. I imagine you would find a collection of containers of anomalous diseases inside a refrigerator in a laboratory with the type of equipment you would expect to find in a laboratory studying diseases.

Add the phrases "are we cool yet?", "does the black moon howl?", "Can't fit round pegs in square holes", and other weird and unsettling quotes from the SCP Foundation into the game. This will make the game feel weirder, kind of like in the game Portal when you find the weird messages written on the walls.

I really think that the game needs to have at least one or two events involving 096. One idea is an event where under certain circumstances there is a very small possibility of 096's face showing up on a screen if you take to long to complete a certain area, (I had a long discussion about this with some other people on this forum and I think that this could work if it is done in a way that is extremely easy to avoid). I also had an idea for an event where 096 would unexpectedly run past you towards an unknown target. I simply think that 096 the way it currently is in the game is too easy to avoid and needs to have at least a few more ways to encounter it. Another idea is to change how SCP-096 is encountered. Instead of simply finding it in a room facing the corner, you might walk into it while it is in the middle of attacking a group of people and seeing what it does to them.
By the way, what happens if another SCP sees 096's face?
Here is another idea, I believe that one very unexpected and definitely scary way to encounter SCP-096 would be to encounter it inside of SCP-106's dimension. Since 096 looks a lot like a human it would make perfect sense for 106 to capture it and attempt to torment it the same way that it normally does to humans. Trapped inside of 106's dimension, 096 will appear to be extremely distressed and confused, although it is still possible to avoid like you would when encountering it normally. When you encounter it in the 106 dimension it will move around whatever room you meet it in and scream whole lot for a short time before quickly exiting. If you escape from 106's dimension after encountering 096 inside it, 096 may spawn in the corner of a nearby room and sit there for a few minutes facing the corner like it's scared before getting up and leaving in the opposite direction as you.
Following that same logic, I think that it would make sense that 173 and 106 would try to attack other humanoid SCPs as well. 173 is unable to damage 106 and will get trapped in the other dimension. While inside the 106 dimension 173 will move very sluggishly and sometimes will still be able to move when you are looking at it. After 173 encounters 106 it's body will be stained black because of the corrosion effect 106 has. If SCP 173 encounters 096, it will attempt to strangle 096. When this is happening you will hear a lot of disturbing noises and 096 will be left nearly dead, but will recover after a while, and it might or might not kill you if you saw it's face while it was struggling with 173 or unconscious.
One other thing about 096 is that you should be able to find a bag or head cover thing to place on it's head since that is how they keep it concealed when it is outside of it's containment room. If you place the bag thing on SCP-096's head it might or might not take it off after a while, or lose it when running into another SCP. You could find 096's head cover next to a dead body near where 096 spawns.
I have an idea for a new room in the game. I think that at some point in the game there should be some kind of room containing a trap. I think that It would make sense for the foundations sites to have booby traps for catching intruders and escaped d class and SCPs during an emergency. Does anybody else have ideas for a trap room? It probably would have to be something that you can avoid if you know where it is or how to recognize it, but would require some skill to get around it, and if you don't know where the trap is and you get caught in it, it would take a while to escape from. You could also use the trap room for catching 173 so that it will not bother you for a while.
I have an idea for an alternate ending to the game. It will be the only good ending to the game, but it will be the hardest to get. In the alternate ending to the game, the player discovers a portal leading into the Wanderer's Library. The portal is invisible and can only be found by obtaining several secret items, and in a regular map this requires that the player go back through areas that you have already been through in order to unlock the items.