When it comes to nicotine extraction the distillation process is the preferred method of removing the natural impurities from the plant based liquid.  Most pharmaceutical grade manufacturers prefer this method and this is the method used to extract the nicotine sold at MyFreedomSmokes. 

An alternative practice is to utilize salt processing to turn the liquid into a sulfate.  This process requires a bleaching agent to remove the impurities and then it is reconstituted with a liquid to turn it back into a useable form.  Due to the bleaching agent introduced in this process, the nicotine sulfate product is often mistaken as being more pure.  This is a common misconception because the bleached liquid appears more clear in appearance in comparison to the slightly tinted freebase derived from the more refined and preferred distillation process.

Freebase nicotine is also a very reactive chemical and it will often change color in solution. In freebase form it tends to be clear with a slight yellow or brown hue. Once mixed, the range of colors it turns depends on what it's mixed with, though pink is typical in PG, and yellow in VG.

Regardless, the color of the nicotine is a purely cosmetic factor.  Nicotine will always have varying shades of color since it reacts over time.  The main agents of reaction are light, heat, and exposure to free oxygen, but different flavoring compounds can also contribute to color changes.  

For best storage conditions, keep it cold, keep it dark, and keep it airtight as this will best mitigate any changes from occurring.  However, don't worry if it darkens as the consistency will be the same and the flavor isn't unduly affected. Even aged e-liquid that has been exposed to ambient light and in a bottle half-full of air should still deliver the same quality nicotine.