You're going to have to ask the developers about the why but I think a gem is just a symbolic representation of a crystal. A gem is a polished crystal after all.
Most people associate PlaneShift with the "Azure Sun" or the Crystal when it comes to a symbolic representation but there is also this (nevermind the outline, didn't mean to leave it):

And a tiny 16x16 version -->

Don't use this one. This is just an example. It's a minute job from the graphic on the main site, which is already compressed and has quite a few artifacts.
Looks funny actually.
Karyuu,
Well, if you guys like that version, by all means, of course. However, keep in mind also, that while it looks detailed at that res, look at how it scales:
This is what it looks like in 32x32 (sharpened when resized), in other words what it will look like on Windows XP desktop:

Fairly ok so far, I guess.
And this is at 16x16 (in QuickLaunch bar, Start>All Programs, and as a "favicon" on the website) -- >

Now this looks way too tiny and golden starts to really clash with blue. And this is with sharpening applied. Without it, it's even more of a blur.
This is why I made the letters go outside the crystal (so, it's still detailed at 16x16) but I still didn't like the clashing between the two colors. To get rid of clashing, you can darken the crystal or lighten the letters or both. But it seems you wanted to preserve the light azure for the crystal, did you not?
Try with larger "PS" letters maybe.
Another solution might be to simply use the gem icon without the letters for 16x16 and "favicon". However, it will still use version with the letters under Linux, since its icons are just .PNG files, so it'll read from the main large version.
It's up to you, of course. With larger golden letters, it might be ok, once you get used to it.
EDIT:It seems you edited your post with a larger version. Here are the results:
Windows XP Desktop -->

16x16 -->

I don't know. A little better, I guess but gold still clashes with blue at lower res - something that I didn't like in my tests.
The white/silver "favicon" -->

Once again, it's up to you guys. If you like it, by all means. I don't mean to discourage anyone.
EDIT2:Karyuu,
Can you make an even larger version with letters as large as possible without being clipped? Also, leave only 2 pixels max on each of the widest sides of the gem to maximize the used space, so it looks larger at 16x16. Also, minimal 2 px shadow or just an online (for those 2px on each side) only, if you can manage it.