The Pathways Into Darkness manual refers to the importance of crystals on a number of occasions. Here are the two main references:

Crystals are objects with special powers. To activate a crystal, double click on it. The word "(Ready)" will appear next to its name. To discharge the crystal, press the Tab Key. Crystals automatically recharge themselves. After each use they recharge more slowly until they finally shatter.

and...

Crystals are very powerful objects. We know very little about them. A crystal must be readied before it can be used. To ready a crystal, double click on its name in the inventory window. The activated crystal's name appears in the player window, below the power bar. The power bar displays the crystal's current power. The power bar must be full before the crystal can be discharged. Press the Tab Key to discharge the crystal. After each use, the crystal will recharge itself.

It is not known how many kinds of crystals you will come across, nor what the effects of most of them are. HINT: The Yellow Crystal is used to talk to dead people. Discharging the yellow crystal while standing on a dead person will initiate a conversation.

Be warned: after each successive use, crystals (except the Yellow Crystal) recharge more slowly until they finally shatter and become useless.

In case you didn't get the message... crystals are powerful but unlike diamonds they're not forever.

But how powerful and how many times can you use them before they shatter?

This section will give you the definitive answers.

Color	Location	Effect	Immune	Uses
	Never Stop Firing	Speak to the Dead	Headless Carlos	∞
	They May Be Slow...	Ice	Ooze Shocking Sphere Sentinel Green Ooze Barney Demon	60
	Wrong Way!	Fire	Shocking Sphere Sentinel Green Ooze Barney Demon	50
	The Labyrinth	Lightning	Wraith Shocking Sphere Sentinel Green Ooze Barney Demon	40
	Watch Your Step	Earthquake	Nightmare Phantasm Wraith Shocking Sphere Ghast Green Ooze Barney Greater Nightmare Demon	30
	Where Only Fools Dare Tread	Petrification	Sentinel Green Ooze Barney Demon	10

Thanks to Hopper in a Story forum post for working out the crystal usage stats. He wrote:

The value stored with each crystal is the charge time. On each use of a crystal, an amount is added to this time, so it takes longer to recharge. If the new recharge time exceeds a set amount, the crystal shatters. Each crystal has a different increment and maximum:

Yellow: initial 300, up by 0 (infinite uses)
Blue: initial 60, up by 2, max 180 (60 uses)
Orange: initial 60, up by 7, max 410 (50 uses)
Violet: initial 60, up by 15, max 660 (40 uses)
Green: initial 360, up by 15, max 810 (30 uses)
Black: initial 10, up by 1, max 20 (10 uses)

These figures match MrM12LRV's in-game experiments with crystals. He wrote at the time:

I've tried moving levels, using crystals before others after they shatter or before they shatter, killing enemies with crystals, using rings, and using a new saved game.

Each crystal is worth two points. Total points to be collected from crystals is twelve.
Only six crystals? Well there is a seventh. The mysterious seventh crystal is the Blue/Yellow Crystal which can be found in the Shapes file of the Pathways Demo vA1. It's not present in the release version of the game. No details are available about its oddly combined heritage.

On the subject of the hybrid crystal, Nexcraft <nexcraft@gmail.com> writes:

What if talking to the dead was originally supposed to happen in real time? Would make defending yourself a bit harder, which might be what the blue part of that crystal is for. Talk to a dead guy, see a baddie coming, and then freeze him with the same crystal. Wouldn't surprise me if someone thought the game was already hard enough and shot this idea down.

Back in Oct 2003, Mark Levin <haveblue@mac.com> jokingly remarked... perhaps it lets you talk to frozen people. :)

The Official Hint Book has this to say about some of the crystals:

Blue, Ice
If you discharge this crystal while a monster is visible, it freezes the monster temporarily. This one does the least damage of all the crystals, but will give you the most uses before it shatters.

Orange, Fire
If you discharge this crystal while a monster is visible, it will burn that monster. This does more damage that the Blue Crystal, but immobilizes the monster for a shorter time.

Violet, Lightning
This crystal affects every monster in a conical area in front of you. It does about as much damage as one AK-47 HE round to each monster it affects.

Green, Earthquake
This crystal only does slightly more damage than the Violet Crystal. It also has a better range, and it affects a circular area centered on you. You can therefore nail creatures behind you with it. However, it takes longer than any other crystal to recharge.

Black, Petrification
One discharge automatically petrifies one monster. The monster gets turned to stone and is out of your way for good. In addition, this is the fastest charging crystal; the first recharge takes under a second. Too bad you don't get it until the very end of the game. In addition, it only works about ten times before shattering.

Ron Hunsinger <listreply1@erstesoft.com> makes an interesting observation about the Violet Crystal found in The Labyrinth:

Every time you enter the Labyrinth, the game completely erases and rebuilds the level. It always starts with an empty cell right in the center, at (16,16), and grows the maze randomly from there. It then puts a Violet Crystal in that center cell, but only if you've never picked one up. It doesn't want you returning here to get more Violet Crystals.

Too bad. :(

Concerning the Black Crystal, President People <presidentpeople@verizon.net> writes:

The Blue Meanie can be killed with the Black Crystal, but the Black Crystal isn't necessarily an instant kill weapon. I've turned the Blue Meanie to stone one time, but at another, run out of charges before he died (No screenshots, unfortunately). My test wasn't that extensive, I was kind just goofing around. My guess is that you should try using it once he's near death.

Through cheating, of course. :)

Of course we need a screenshot to verify this account. :)

Back in June 2001, "Still Thinking" in a Story forum post made an interesting discovery while talking to Muller on "Happy Happy, Carnage Carnage". It is generally believed that the Germans knew nothing about the crystals in the pyramid. If you ask Muller about the "Crystals" he'll reply:

I know nothing about the crystals.

However "Still Thinking" noted that if you use the words "Blue", "Yellow" or "Violet" you'll also get the response:

I know nothing about the crystals.

So it would appear that Muller DID know something about the crystals. Well that's Muller for you. ;)

Back in Feb 2000, Matt Heath <PoetOTR@aol.com> wrote concerning the Green Crystal:

Why does the player get hurt when a Ghast causes an earthquake, but doesn't get hurt when starting quakes himself with the Green Crystal? Not too consistent, is it?

President People <presidentpeople@verizon.net> provides a screenshot of a petrified Blue Meanie. While the Black Crystal is the most powerful crystal it still won't kill the Blue Meanie outright before it shatters. You first have to soften him up with another weapon and then finish him off with the (cheated) Black Crystal.

President People also provides screenshots of the Blue Meanine being defeated by Fire and Ice.

Ron Hunsinger <listreply1@erstesoft.com> provides some details about how Crystals work and which monsters are immune. These are based on his observations of the Pathways code.

The Yellow Crystal, of course, does no damage.

The Green Crystal hits all hunters, regardless of distance or direction. It can even hit hunters behind you or behind walls. But remember, although there can be as many as 60 critters on each level, at most 12 of them can be "hunters" (my term) at any one time. Only a hunter can have a strategy, only a hunter can attack, only a hunter can be animated, only a hunter can be hit. All the other critters on a level may as well be moss on the wall as far as the game cares. Roughly speaking, critters become hunters when they're born, when your light touches them or a sector next to the one they're in, when you get within two sector of them, or when they hear a shout and are not in an ambush zone. Hunters stop being hunters when you leave the level, or whenever they can't see a path to you (they do not actually have to see you), or whenever there are 12 other hunters nearer to you, or when they're dead. A dying hunter remains a hunter until it's dead, so that its death throes can be animated (and so it can act as a shield against the knife), but otherwise may as well not be there. Flying rats and amphibians are neither critters nor hunters.

The Violet Crystal has exactly the same fire pattern as the frag grenades. It'll hit every hunter any part of which is visible in the middle half of the screen.

The other crystals have the same middle-of-the-screen spread, but only hit the nearest such hunter.

Remember that you can't see beyond the range of your light, or through secret walls. If you can't see it, you can't hit it. You are, however, assumed to be able to see through anything that isn't a wall. Pillars, for example. Some are short enough for you to see over; the game assumes you can see through (and shoot through) all of them.

Crystal damage is chosen randomly (using a uniform distribution) from the following ranges:

Blue 20..34
Yellow N/A
Orange 55..64
Violet 90..119
Green 100..199
Black 10000..10999

Crystal damage is not affected by distance. The Violet and Green crystals, which can hit more than one hunter, calculate the damage independently for each one.

Hitting a hunter that is immune to that crystal does zero damage, but still counts as a hit.

The Purple Barney, Venomous Oozes, and Dreaming God are immune to everything (except at the end when the Dreaming God becomes vulnerable to weapons but still not to crystals). Other immunities are:

Blue: Oozes and Shocking Spheres
Orange: Shocking Spheres
Violet: Wraiths and Shocking Spheres
Green: Nightmares, Phantasms, Wraiths, Shocking Spheres, Ghasts, Greater Nightmares.
Black: none.

If you want to see The Big Blue Meanie flinch then you are going to need to use a crystal. xcalibur posted the following pics to show the The Big Blue Meanie flinch sequence after being hit by the Orange and Violet crystals. The Blue crystal causes no flinch sequence.

So now you know how to hurt The Big Blue Meanie.