ThomasSpeedrunner's Custom Sprite Gallery

[Vipershark]

As far as the palette on the gems goes, you did a decent job with the desaturation, though I think you may have gone a bit too far with it. Bring the saturation up just a bit.
In addition, they could still use some more contrast.
You did absolutely zero hue shifting, though.

I'll bring up SchAlternate's gems again.

Note how the yellow gem goes from a dark brownish yellow with a hint of orange up to a nice golden yellow, to a soft bright yellow.
Note how the green gem goes from a dark brownish green and then ramps up to a soft yellowish green.
Note how the teal gem goes from a dark blue-ish turquoise to a light greenish teal.

Let's take your red gem as an example.

Look at the color picker in paint. What you've done is simply move the color selector up and down, but you haven't changed your hue at all. For each of your shades, the hue is still zero, which is a flat red.
What you need to do, in addition to changing saturation (up and down on the color picker) and brightness (up and down on the slider), is move left and right on the color picker to change your hue as well.

Darker shades hue shift to cooler colors, while brighter shades hue shift to warmer colors.
In the case of red, you can hueshift down to, say, the purple region for dark shades, while your light shades can hueshift up as high as orange or yellow.

You need to use all three axes of movement (left/right, up/down on hue/saturation grid plus up/down on brightness slider) to pick colors that work well, not just one or two.

I guess the easiest way to describe it is that you almost want to be moving diagonally on the grid to pick the general area for each shade and then using the brightness slider for fine tuning, but every palette is different so that might not always apply.

Your lack of hue shifting is especially evident on the yellow and dark blue gems, but all of them need it, not just those two.

Another thing that I would suggest is giving your gray crystal a bluish tint.
I'll bring up SchAlternate's examples again. If you open it in paint and look at where the shades in his gray crystal are, they all fall within the blue/turquoise region of the color grid.
Most sprites don't actually use flat white, gray, or black. Instead, they use extremely desaturated blues which, when done correctly, give off the impression of white, gray, and black. Plus it's much easier on the eyes and looks much better.