in my preliminary research on gems, it seems like imperfect gems can actually cause harm (or at least, not be beneficial).  i immediately thought about some jewelry that i have (specifically some amethyst, since that is my birth stone) that is imperfect - the stones have either become cloudy over time or unbalanced in color.  obviously, i won't be wearing these, but i wonder:  what should i do with them?  is there a way to properly "dispose" of imperfect gems?

If you really believe they are imperfect then the best thing you can do is to give them away. Personally I do not see any gem or crystal, rock or stone as imperfect. We are all imperfect. That some people believes that a gem has to be perfect to work is beyond me, its absoloute superstitious rubbish designed to make you pay more.

okay, can you clarify something for me please?  on this thread, you stated something about "incurring the wrath of imperfect gems".  if no gem is imperfect, what did you mean by this?  *confused*

Gem is right there is no such thing as imperfect. They are just as individual as we humans so if this is imperfect then everything that is created is imperfect.
If you go to a jewelry store they will sell you gemstones based on clarity for instance  a diamond is rated in how clear it is and then the color and then the shape and so. A stone rated SI (Slight Inclusion )is not as good as IF (Inclusion free) which is the one everyone wants. To me the inclusions are the personality of the stone. Gemstones, crystal, trees, herbs, fish, birds are all individuals each has their own unique personality and as my people do , we call each of these people as well they are just dressed different than us two-legged beings(that's human). So if you do not want to use them then give them to someone as Gem stated.
Now for the other thread I believe Gem was stateing that using the wrong stone for something is how he was refering to the imperfect stone, but this is my opinion he will have to clarify it in his words.
I hope this helps you.

I was being sarcastic lol. I don't believe in the wrath but many do seem to have a very strong belief in what they are told about 'imperfect gems'.

But thats the view from a geologist and crystal healer rather than a religious gemologist.