[Intentionally Wrong]

Metroid Prime's the obvious example. The investigation the player does of the planetary circumstances is tied to the player's exploration; the mechanic is a simple matter of switching to scanner mode and scanning appropriate wall tiles. It's pretty good, since the investigation element is a little important but there's far more information available to the player who wants to find it.

I'll leave Deus Ex to the people who've played more of it, but it does strike me as a more RPG-like approach.

Anchorhead is the high-watermark for investigation in Interactive Fiction; the review I linked even describes the pitfalls investigation in games often comes up against:

[Intentionally Wrong]

I'd say you could make that case, yeah. Silent Hill is kind of an odd case because it jumbles up the hidden game resources and story resources in the same way. That's something RPGs are trying to move away from--that sense of "I have to talk to every NPC in this town so I don't miss out if one of them hands out items!" Likewise the constant hiding of treasure chests around the outer bounds of the game world, which just draws attention to the world's artificiality. I find Deus Ex's approach of focusing game and story rewards in the self-evident obstacles of locked doors and skeptical NPCs more immersive.
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JSNLV is frequently and intentionally wrong.