Age, breed, conformation, height, color, breeding/lines, health(health problems or previous injuries), temper, the area you live in, what the demand is and what is available, the horse population local to you, the economy.
A horse that sells for $3,500 here locally won't sell for anymore than 1,000 in certain areas. In Europe, you can buy registered and absolutely outstanding warmbloods for a third of the price of how much you would pay here.
Horse prices, like most other things, are only as valuable as what someone is willing to pay, and vary tremendously due to a large number of factors. Around here, here are ranges for registered horses, excluding under $1000 or give aways that sometimes turn up very good horses.
$2500-$3500 - A good disposition horse, green to limited experience, but that you can ride from day one and don't need to invest in any more training unless you want to.
$3500-$5000 - A experienced, seasoned, go anywhere horse, typically 10+ yrs old.
$10,000-up - Horses with good show records or promising show prospects.