The most rare AND expensive ponies are the SA and Takara ponies. They rarely come up for sale, maybe 2-3 a year. SA ponies can reach $1500-$2000 and Takara ponies $1000-$1500, a piece!
Some ponies are equally as rare (or even more), but are not so sough after. That's why they not always reach the price as a SA or Takara. I'm talking about some hair-color variations, for example French windy with purple hair. She came up for sale once within a year, but she only reaches the $600-$700 mark.