There is no universal clarity/color grading standard for colored gemstones.  They can be graded in a similar way to diamonds with some significant differences. Color, clarity, cut, and weight are the main value factors. The difference is that these factors are evaluated and weighted differently than in diamonds. In colored stones, color is the main consideration (most dealers assess the color component of a stone at between 50% to 70% of its value) .

Unlike with diamonds, a minor clarity difference rarely affects the price of colored stones, and in some cases a stone can be valued more with a lesser clarity grade. A sapphire for example with a rich "velvety" type color is preferred over one that has a diamond like transparency even if that means the stone might contain minor rutile internally.

Below you can find the GIA clarity charts for colored stones. One thing you might notice, there is no flawless rating for colored stones, the argument is that by looking with high powered magnification, you can always find a spot, crystal growth, included crystal, or something if you look hard enough, since they are natural stones.

 

GIA Type 1 Clarity Chart

VVS Very Very Slightly Included - Minute to not detectable
VS Very Slightly Included - minor
SI1 Slightly Included - NOTICEABLE to obvious
SI2 Slightly Included 2 - OBVIOUS to noticeable
I1 Included 1 - Prominent - moderate effect on appearance or durability
I2 Included 2 - Prominent - severe effect on appearance & durability
I3 Included 3 - Prominent - severe effect on beauty, transparency & durability
Type 1 Gemstones are gemstones that are normally found to be clean.  This includes gems such as Amethyst, Aquamarine, Blue Topaz, Citrine, Kunzite, Tanzanite, Yellow Beryl, Yellow Chrysoberyl and  Diamond.
 
 

GIA Type 2 Clarity Chart

VVS Very Very Slightly Included - Minor inclusions
VS Very Slightly Included - NOTICEABLE to Obvious
SI1 Slightly Included - Noticeable to OBVIOUS
SI2 Slightly Included 2 - Obvious to Prominent
I1 Included 1 - Prominent - moderate effect on appearance or durability
I2 Included 2 - Prominent - severe effect on appearance & durability
I3 Included 3 - Prominent - severe effect on beauty, transparency & durability
Type 2 Colored Gemstones by their nature have natural inclusions. (Inclusions are the norm) This includes gems such as Andalusite, Crysoberyl, Alexandrite, Corundum (i.e. Sapphire and Ruby), Garnet, Peridot, Quartz, Amethyst, Citrine, Ametrine, Spinel, Tourmaline and Zircon.
 
 

GIA Type 3 Clarity Chart

VVS Very Very Slightly Included - NOTICEABLE to obvious
VS Very Slightly Included - Noticeable to OBVIOUS
SI1 Slightly Included - OBVIOUS to prominent
SI2 Slightly Included 2 - Obvious to PROMINENT
I1 Included 1 - Prominent - considerable effect on appearance or durability
I2 Included 2 - Prominent - severe effect on transparency or durability
I3 Included 3 - Prominent - severe effect on beauty, transparency & durability

Type 3 Colored Gemstones by their nature have many natural inclusions. (Heavily Included is the norm) This includes gems such as Emerald,  Beryl, Rubellite, and Tourmaline.

 

A rather nice guide for buying gemstones can be found online  on the G.I.A. website, Click on this link to read How to Buy a Gemstone