There must be an active magical effect in place to pick up something with detect magic. A familiar by itself, AFAIK, does not generate an aura.
The rules are a tad unclear, though. Supernatural abilities, spell-like abilities and spells are all magical. There is no rule (that I can find) that states that all three of these things generate magical auras, but I'd rule it that way.
As a result, I'd say that a familiar that has an active empathic link, a familiar that is holding a touch spell or a familiar that is being scryed by his master would show up. A familiar under the effect of a spell would also show up. Beyond that, I'd say no.