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Puzzle Agent is... an adventure... game... with logical puzzles. But I doubt it's what you meant.

But quite often, the tone and settings determine how logical the puzzles are. Games taking place in absurd universes tend to have absurd solutions. Older games went for "oh god how was i supposed to guess that" lulz, newer games have internal logics, or ways of thinking, that allow you to see the fitting solutions more easily : the Sam & Max series felt "logical" enough to me (that may say more about me than about the games though).

In a different way, Full Throttle was down to earth enough, if I remember well. It had humour, was set in a weird post-apocalyptic-ish world, but was grounded in materialist logic.

But often, games that are set in a realistic world (more movie-inspired than comics-inspired), and go for a serious tone, try to no break immersion with absurd gamey lol solutions. And that may be games such as the Deja Vu series, or Borrowed Time (if I remember well), or, as already mentionned, the later episodes of the Holmes series, the Blackwell and Shivah games, etc. Even the old Police Quest games were realistically logical (sometimes even too much, as it punished you strongly for not following real-life police procedures). Generally, non-parodic detective stories are a safe bet, be they set in the past, present or future. It may apply to the Tex Murphy games, but I haven't played them yet. It was the case, if I remember well, for the very bladerunneresque Rise of the Dragon, and the even more bladerunneresque Blade Runner.

And even some pure fantasy titles can feel logical. I think it was the case for Syberia. As far as I remember, most of its solutions were obvious at least in hindsight. Which was part of its very own "grounded poetry" atmosphere.
Surprised there was only one other recommendation for Loom.
The great thing about Loom is that once you understand the system, all the puzzles make total sense. And the system is very simple:
It has no inventory, no weird item mixing puzzles, you just explore your surroundings to discover patterns (basically spells), and then figure out how to use those patterns to solve the problem at hand, and unravel a beautiful story.
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babark: Surprised there was only one other recommendation for Loom.
The great thing about Loom is that once you understand the system, all the puzzles make total sense. And the system is very simple:
It has no inventory, no weird item mixing puzzles, you just explore your surroundings to discover patterns (basically spells), and then figure out how to use those patterns to solve the problem at hand, and unravel a beautiful story.
And I forgot to mention that there's also Olav and the Lute. It hasa very similar mechanic to Loom, so is likewise perfectly sensible once you get it. It's very short, but really good and free.