I would say that colors should be limited by time frame, and only so many should be allowed per user. These two limits would exist to ensure that these colors retain their values.
A time frame of maybe one full month once per year, every year sounds fair to me. That way users have a chance to do these quests even if they have jobs and school occupying them most of the time.
I stated earlier that five or six "quests" to obtain these colors should be allowed for all users. Now that I'm thinking about it more in depth, ranchers should naturally have more turns or "quests", so to say. Ranchers need every opportunity they can get to raise sellable pets. Just like how ranchers have more hatches than merchants, they should have a few more turns to obtain limited colors.
I agree with Tryst's view that the design should not be a flat color. Some people probably think that this concept involves a lot of work for pets to be completely redrawn in all three stages. This isn't necessary. The original lines can still be used. A few things can be added to original lines in addition with a color change. To save the time of artists, the quests can be set up to where only adult pets will be allowed to be changed. The Regression Ray won't work with pets that are limited colors.
Now something I'm not sure about is what pets will be eligible for color change. There are two options.
The first: Either one or two pets per year like Gondra and Easero for 2010, Kayoki and Ebilia for 2011, and so forth. Notice I paired an average pet with a seasonal pet. CS and Uldavian pets would be discounted from this. This is another time-saving option for artists.
The second: All average pets (either adult or all three stages) will be eligible for color change. This would require a lot more work, and I wouldn't recommend this until the site grows larger and more artists are hired.
There is a lot of room for discussion. Anything is possible, really. These are just some of my ideas on how these events will work.
The next question is: What do users do to get limited colors?
I originally though a NPC quest for items would be good. This helps out merchants.
To change things up, we could have "tasks" that users do to earn color changes. For example, donate five items to the Trash Isthmus, pick three flowers from the Atqueen Forest, obtain five secret avatars, intiate one pet trade request, etc. These would be tedious for more experienced users though they would help newbies out.
I dunno. xD I'd be happy to hear other people's suggestions.