I've already mentioned that it's sometimes believed that pinto horses are more docile (there's some evidence this one might be true). The Roma prefer them. Some Native Americans also believe spotted horses (both pinto and Appaloosa) are lucky - and, in fact, this is the origin of the Paint and Appaloosa breeds, as the superstition spread to white cowboys and made the colors desirable.
In England, horses with blue eyes are thought to have vision problems or to be blind - this is not true. There is also no known association between eye color and hearing problems in equines.
Also in much of the English speaking world, chestnuts, especially mares, are viewed as more hot and reactive, perhaps an extension of the superstition that human redheads are hot tempered. But there are still horsemen who will not buy a chestnut mare, especially if she's Arabian or Thoroughbred. However, there are a lot of chestnut Arabians because the Arabs apparently believed they had more courage. The Arabs also believe that a "bloody shoulder" mark, sometimes seen on grey horses, is a sign that Allah's favor is on the horse.
Another one is that dark or striped hooves are stronger than light colored hooves - there's no actual difference other than pigment, according to science, but I have to admit I've seen more hoof cracks on the light hooves if a horse has both, so...
Oh, another good one: "One buy him, two try him, three look well about him, four live without him" - which refers to white socks or stockings and is connected to the myth that light colored hooves are weak. It's most often heard on the racetrack. Another variant is "One sock, buy 'em. Two socks, try 'em. Three socks, deny 'em. Four socks, don't buy him!" (Dressage people, however, try to avoid horses that have a sock on only one side because it can make the horse's action look uneven and cost points).
White horses are lucky in some cultures and unlucky in others. In some Hindu marriage ceremonies the groom goes to his fate riding a white horse accompanied by the youngest male in his family. Modern western weddings sometimes have the bride arrive in a carriage pulled by white or grey horses. But in Britain, white or grey horses are sometimes seen as "fetches" - omens of death.
(I realize most of these are British - it's where I grew up). The racing industry is, as mentioned, prejudiced against horses with too many white legs, but it's also believed in some places that white hairs in the top of the tail, called a "skunk tail" and associated with rabicano, make a horse faster.
Anyone got any I don't know about?