Certain colors aren't available for certain species simply because the neopets artists haven't drawn them yet. Neopets releases one or two new colors for each species on their special day, like how flotsam day was a couple days ago and they received the new "toy" color, which they could not be painted before. So you might want to check the neopian calendar to see if it's worth waiting - for example if it's an ixi you want to paint, Ixi Day is July 11th, so you could wait to see if they get the oil color on that day.
If you want to see all the colors that are available for each pet, on the TDN website you can go to the customization tab and select "color/emotion" database. This will allow you to see all the colors available for each pet, it has really helped me make these tough choices in the past.