When a Wizard likes to search every shelf with books for magical tomes and scrolls, do you roll Investigation or Perception?

I would use Investigation... for anything active where the character is delving for something, I use investigation. For more just standing looking around, or listening, I use perception.

I've always kind of gone with the advice of: If it's something the character can't see; perception. If it's something they can; investigation.
Alternatively - if they're just looking around; perception. If they're physically rummaging around; investigation.

Obviously those are just rules of thumb so not applicable in every situation - but for yours I would definitely say investigation. Not only that - but it would take some time to thoroughly search.

I would use investigation if the Wizard is going through the bookshelf, looking for scrolls, spells or research into a school of magic.

I would use perception if they are at a distance and just casually glancing to see if they see anything like it. 

Looking for something specific would be investigation.

Perception is trying to see if anything changes around you, or look for a general occurrence of sound 

I'd use investigation.

My rule of thumb - could an animal, like a keen-eyed hawk or a bloodhound with an excellent nose or an owl with great hearing, do this really well? If so, perception.

Could Sherlock Holmes - a human with normal senses, but with an excellent brain for understanding how things fit together and encyclopedic knowledge of whatever scholarly field is relevant - do this really well? If so, investigation.

In this case, searching for scrolls isn't about having really excellent eyesight and "seeing" a tiny scroll hidden somewhere - it's about going through the books and based on a cursory look, quickly understanding which ones are scrolls or spellbooks that the wizard can use. A hawk would have no idea (and its keen senses would be unnecessary), Holmes would instantly be able to pick up which ones are actual magical tomes by looking at the first page.

So, investigation.

Which is higher... your int or wis modifier, do you have proficiency in either... go with the highest mod.

In your case I'd use perception. 

In my game.

Passive perception tells the players what they see going into a room or area. 

Rolling perception to see things like hidden walls or a hidden safe or other hidden items or a tree that's just out of the ordinary. 

Then roll investigation to figure out how to get into that hidden thing. 

My players like to roll dice. A lot! I'm perfectly happy to accommodate them. 

There was a scenario like this one I was going to raise with my DM after asking a party member to use his ability with people to see if anyone in the tavern seemed "on edge." He [the party member] was called for a perception check on what I was expecting to be an insight check instead - he got a good enough roll for it so I didn't complain out loud but in my head I was thinking it was a bit odd. Afterwards I kinda shrugged my shoulders and figured his game, his rules. It was my personal DM opinion that got ahead of me and thankfully I didn't push for it.

Quote from ftl >>

I'd use investigation.

My rule of thumb - could an animal, like a keen-eyed hawk or a bloodhound with an excellent nose or an owl with great hearing, do this really well? If so, perception.

Could Sherlock Holmes - a human with normal senses, but with an excellent brain for understanding how things fit together and encyclopedic knowledge of whatever scholarly field is relevant - do this really well? If so, investigation.

In this case, searching for scrolls isn't about having really excellent eyesight and "seeing" a tiny scroll hidden somewhere - it's about going through the books and based on a cursory look, quickly understanding which ones are scrolls or spellbooks that the wizard can use. A hawk would have no idea (and its keen senses would be unnecessary), Holmes would instantly be able to pick up which ones are actual magical tomes by looking at the first page.

So, investigation.

I love this rule of thumb... it's basically what I do but you formulated it so much more clearly than I ever have.

Are you already aware of the thing?

If yes, investigation. If no, perception.

Investigation! And here's why: 

If your character is looking for something specific, i.e. they have an objective in mind during their search, this is investigating. Hence, investigation. 

If your character isn't looking for anything specific, but just having a look around for...anything interesting, what they find will depend on what they perceive of their new surroundings. Thus, the check to make is perception. 

Hope this helps, and great question! As a DM I've had to give this a good deal of thought myself during gameplay. 

I like the hawk vs. Sherlock take, that's a good way to sort out which sense is best used for a roll.  Perception vs. Investigation trips up a lot of tables.  I think I'm going to bring that comparison to my own table and see what they make of it.

The Insight note is apt as well; Insight is a difficult skill.  Players should absolutely describe actions rather than ask for rolls, but most typical uses of Insight are difficult to describe beyond "am I buying this horse manure?"  It doesn't help that uses of Insight beyond "Lie Detector" tend to be murky and poorly defined.  I've disliked that for quite some time and have been trying to figure out where Insight should fit in the sensory spectrum, especially since "Lie Detector" is a shitty use of a skill and often handled poorly at the table anyways.  The idea of using Insight over Perception when trying to 'read the room' and discern the mood of a crowd is great.  That definitely suggests where Insight should be more helpful than Perception.

A keen-eyed hawk knows where predators and ambushes are, and can easily locate discrepancies in a space, but the hawk can't tell a book from a tree stump and has no idea what the bipedal monkey-things in that space are doing.

Sherlock Holmes can see connections, apply his intellect and knowledge to a room, and know what went on in that room for the last six months as well as where all its secrets are, but he's as clueless as the bird (in this theoretical, anyways) as to what other people are thinking or feeling and he's as vulnerable to a well-hidden ambush as anybody else.

Deanna Troi can walk into the space and tell whether the people in it are nervous or not, tell where their attention is and who seems to be the center of the group, and observe moods and relationships, but she has no idea where the hidden trap door is, nor where the ambushers waiting to drag her to yet another Comic Con are.

Hmm.  Good start, methinks.

Quote from Yurei1453 >>

I like the hawk vs. Sherlock take, that's a good way to sort out which sense is best used for a roll.  Perception vs. Investigation trips up a lot of tables.  I think I'm going to bring that comparison to my own table and see what they make of it.

The Insight note is apt as well; Insight is a difficult skill.  Players should absolutely describe actions rather than ask for rolls, but most typical uses of Insight are difficult to describe beyond "am I buying this horse manure?"  It doesn't help that uses of Insight beyond "Lie Detector" tend to be murky and poorly defined.  I've disliked that for quite some time and have been trying to figure out where Insight should fit in the sensory spectrum, especially since "Lie Detector" is a shitty use of a skill and often handled poorly at the table anyways.  The idea of using Insight over Perception when trying to 'read the room' and discern the mood of a crowd is great.  That definitely suggests where Insight should be more helpful than Perception.

A keen-eyed hawk knows where predators and ambushes are, and can easily locate discrepancies in a space, but the hawk can't tell a book from a tree stump and has no idea what the bipedal monkey-things in that space are doing.

Sherlock Holmes can see connections, apply his intellect and knowledge to a room, and know what went on in that room for the last six months as well as where all its secrets are, but he's as clueless as the bird (in this theoretical, anyways) as to what other people are thinking or feeling and he's as vulnerable to a well-hidden ambush as anybody else.

Deanna Troi can walk into the space and tell whether the people in it are nervous or not, tell where their attention is and who seems to be the center of the group, and observe moods and relationships, but she has no idea where the hidden trap door is, nor where the ambushers waiting to drag her to yet another Comic Con are.

Hmm.  Good start, methinks.

 Goes exactly, how I rule that on my table.

My rule of thumb is "could my dog do it? Perception". In the case of searching shelves, if the goal is to notice things like scrolls that have fallen behind a row of books, sure, perception, but if you're running through the books trying to figure out what they are I'd actually use arcana.

Quote from Lyxen >>

So what do you think about this take on the subject ?

My interpretation of the rules are: Perception: your monkey brain in action. Investigation: a scientific conducted research.

If the evidence of what you're looking for is not presented, then you roll Perception. If it is, then you roll Investigation.

Lets take my Wizard example: 

What is the evidence? A bookshelf with many books in plain sight.

Hypothesis: There is arcane knowledge in those books.

Experiment: Rolls Investigation to go through the books, using Arcana knowledge to find anything useful to copy to a personal Grimoire.

Conclusion: Most of the books are about monster anatomy. There are very few used arcane tomes, with pages destroyed from the deciphering process, indicating that another wizard has looted this place before.

I'll use my free action to look for vestiges of the wizard who's been here before 

What is the evidence? Unknown. An old room, full of old broken furniture.

Rolls Perception to find evidence of a recent visitor

You sniffed a burning smell and found beneath a table in the corner, a recently used torch.

Theory: There was another adventurer in this dungeon, a scholar of magic that recently looted this place.

Hypothesis: the wizard is still alive.

What is the evidence? unknown. The dungeon continues to descent from a small corridor ahead.

Rolls Perception to find any signs of movement through that corridor

You found nothing. 

New Hypothesis: That wizard is dead, and his Grimoire is somewhere in this dungeon, waiting to be claimed.

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That is usually how my thought process goes when we're playing Sherlock Holmes in this game.

Quote from Pantagruel666 >>

My rule of thumb is "could my dog do it? Perception". 

Okay---this is like a perfect answer in a nutshell!