Magic Circle against Evil is a chain spell from Protection from Evil. It says, "Third, the spell prevents bodily contact by summoned or conjured creatures. This causes the natural weapon attacks of such creatures to fail and the creatures to recoil if such attacks require touching the warded creature. Good elementals and outsiders are immune to this effect. The protection against contact by summoned or conjured creatures ends if the warded creature makes an attack against or tries to force the barrier against the blocked creature. Spell resistance can allow a creature to overcome this protection and touch the warded creature"
In the Shadowdancer description it specifically says, "Summon Shadow: At 3rd level, a shadowdancer can summon a shadow, an undead shade. Unlike a normal shadow, this shadow’s alignment matches that of the shadowdancer. The summoned shadow cannot be turned, rebuked, or commanded by any third party. "
It seems pretty clear to me a Magic Circle will block a Shadowdancer's companion.
As for familiars, "Familiar: A sorcerer or a wizard can call a familiar. Doing so takes a day and uses up magical materials that cost 100 gp."
Familiars aren't summoned, though they are "called." While a case could be made that familiars are called via some sort of calling spell*, it's a class ability not tied to a spell. Unlike Druid's and Ranger's Animal Companions which is clearly tied to Animal Friendship. Calling in this case seems to be done via a ritual that while it's magical in nature, and the familiar is a magical beast, the process isn't specifically covered by the normal spell-like rules. In other words, a Familiar doesn't vanish in an antimagic field whereas a Shadowdancer's companion would probably be temporarily dispelled by an antimagic field.
I can certainly see either ruling, but I think a strict interpretation of the rules conforms to what I've outlined above.
Hope that helps,
Greg
*Calling: The spell fully transports a creature from another plane to the plane the character is on. The spell grants the creature the one-time ability to return to its plane of origin, although the spell may limit the circumstances under which this is possible. Creatures who are called actually die when they are killed; they do not disappear and reform, as do those brought by a summoning spell (see below). The duration of a calling spell is instantaneous, which means that the called creature can't be dispelled.