Part of a Boss Creature that flashes red- Usually mean "shoot this" to the player.

Or more generally, anything that stands out too much in a character is assumed to be it's weak spot. Like that jewel incrusted in the middle of the chest. Or the glowing eye.

Here are some sounds that I think would be symbolic.

Weird humming noise: Power core, probably close to objective
Utter silence: Something bad is going to happen

Just my (litterally) 2 cents.

I think this should be made into a sticky.

enemy flashes when you shoot them: you damaged them (e.g. when fighting a boss with a vunerable spot, to let you know that you hit it)

Numbers on top of NPCs if you hit them: Numerical representation of damage done to them.
Specially big, flashy or in a strange color numbers on top of NPCs if you hit them: Numerical representation of damage done to them and managed to do a critical hit or hit a weak spot.

Hey that's an excellent idea, but are you interested in the underlying symbolism, or the more straightforward conventions.

So far the posts list what I would call cliches, conventions that have been used throughout gaming history.
Stuff like colour coded enemies. Guys with the same appearance, but only different colours to show that they are stronger versions of what you used before.

If you are thinking of deeper concepts... mmmh... that would be more interesting, but I think a bit harder to analyze.

Oh, I just went through your post again. Right, things that have taken their own particular meaning in the context of games.

Well, food items !
So often you kill monsters and suddenly food items pop up, giving you points. Do you remember a game like Prehistorik ? Going around collecting food for your tribe. Or Commander Keen ?
The food item becomes a Pavlovian symbol, a treat you give to a good dog as a reward.

I am sure SunAndShadow would have something to say about all this [grin]

I looked at Symbols.Net but they don't have gaming symbols there, nor at Symbols.com