Art is really hard to fix a price for. Basically, its worth as much as people will pay for it. Some customs go for big $$ but they are probably masterfully made and by someone who is in demand and has a well-established name as a customizer.
Some people start out thinking they'll make a killing, but it takes a long time to establish your name as a great artist, even if you do have the skills to make amazing ponies.
Another factor is fan base. For instance, a Dr. Who pony that looks like the 10th Doctor will have not only pony fans, but Dr. Who fans as well.
Then there are the regular supply/demand rules that apply as well. When g4s first started, Muffin Pony customs were SUPER popular. Now there are some regular releases of her and she's not as big of a deal. A Princess Luna custom might go for more than a Pinkie Pie custom, but then again you have to consider how many people have Pinkie Pie armies that they are willing to spend on.
My advice is to ask a professional customizer what they think your particular pony might sell for and if you think you want to start low, you can always say 'SALE!' that way you can raise prices for the next one if needs be. Pricing art is an art in itself. Best of luck!