There are 4 factors when bulding a defense of Fair Use to consider -
The purpose and character of the use, including whether such use is
of a commercial nature or is for nonprofit educational purposes;
The nature of the copyrighted work;
The amount and substantiality of the portion used in relation to the
copyrighted work as a whole; and
The effect of the use upon the potential market for or value of the
copyrighted work
These four factors often play differently weighted roles from case to case,
See American Bar - Satire/Parody Fair Use
It would probably be really hard to prove damages from such "infringement".
The main idea behind copyright is to protect the vested interest of the copyright holder from losing value due to someone stealing the holder's work and passing it off as their own. Without a copyright law, the stealer could gain profit from the holder's work and the holder would have no legal recourse to gain back the lost value. When referencing other's work, you have to consider, does their work benefit from your perspective and provide mutual gain, or does your work benefit from the reference and hinder their's?
One example would be a character calling out another character: "Dude,
why on Earth are you hiding in a stupid box?" (a reference to hiding
in cardboard boxes from Metal Gear).
Consider the factors:
1 - purpose of this character is commercial in nature, as even if it's a small event in your game, everything about it would be a commercial for the game
2 - no actual work is being copied here, only a reference to an idea
3 - no amount is copied, again only an idea is used
4 - one could hardly claim that MGS series would be out any consumers due to a minor reference in your game
Now for extreme contrast suppose you had this example:
A character calling out to another character, who has a mullet and is
smoking a cigarette while dressed in tactical sneaking gear, "Folid
Flake, why on Earth are you hiding in a stupid box?"
Consider the factors:
1 - purpose of this character is commercial in nature, as even if it's a small event in your game, everything about it would be a commercial for the game
2 - the persona of Solid Snake is clearly captured in this work,
3 - the combination of the hair style, personality trait(smoking), similar appearance, and very close sounding name create a large portion of copied work,
4 - it is possible that some potential consumers of MGS thought your work was a legitimate MGS work, and those consumers only purchased your product because they thought it was Solid Snake
In the first example, it would probably be very easy to win the defense case of Fair Use due to each factor strongly favoring the defense.
In the second example, the case could go either way, and depends on how strongly each factor was argued and how much it was shown to weigh into the argument. It's key to remember that copyright claims are 'reactive', so a copyright holder has to feel infringed upon to enact it. Therefore, the "grey area" cases are only an issue when actual damages are occurring.
In any case, an extreme example, like one where Solid Snake's persona was so accurately copied that you would think Konami/Kojima was credited but was not, is a clear violation.