whoops.  okay, my bad.  guess i simply need to do more research.  thanks for answering all of my questions!

No problems, even after nearly 50 years I am still learning more every day

Gems that are eye clean can be considered good and auspicious and one should only wear eye clean gems.By eye clean i mean that gem shold be free of cracks,impurities and should hav brilliance and lusture.Gems that are crystalls such as ruby,sapphire,emerald,etc should be transparent.opaque gems should not be worn.

Jyotish gemology definitely concerns itself with the condition of gems - they must not be included, they must not be treated, there's usually a carat minimum...but if you're talking about crystal healing, then a stone doesn't have to be perfect - if it feels right to you, then it will help. As for disposing of them, I would probably just bury them in the ground - give them back to the earth.

I'm a couple of months behind with a posting in this thread but members interested in gems/gemstones etc should always be wary of the semi-precious ones that might have been colour enhanced and which will invariably fade over time. If colour is a factor in gemstone healing etc, it should be a natural/original colour, not an artificially induced one, as that would undo the effect the natural gemstone is supposed to impart.
I always distinguish between gems and gemstones by their cost....gems are really expensive (diamonds, emeralds, rubies etc) and gemstones are affordable (amethyst, jasper, bloodstone, citrine, rose quartz etc).
Imperfect gemstones I often see are those "amethyst" which are chemically dyed clear quartz, and although ametheyst is in the quartz family, its natural colour is formed by natural chemical infusions over millions of years. Also, the dark yellow "citrine" is most likely to be amethyst heated to about 400 degrees, not the pale yellow ones used in quality jewellery.  
When Cassienyc expressed concern over her Amethyst fading, it may have been due to her stone being artificially coloured.
Other examples are when milky Chalcedony is dyed various colours and sold as green or blue agate, and particularly, Aventurine when its dyed an emerald green.
So yes, there are many imperfect gemstones, but when it comes to imperfect gems, that's for the experts to determine, but each imperfection in those stones are also their signature for identification in the event they're stolen - most valuable diamonds and emerals are identified by their imperfections.
I love all gemstones and have trouble with the ones designated for specific days of the weeks, months of the year, astrological signs etc....why can't we just have the ones we love, not the ones someone says we should have?

Zircon