In our dojo (Kung Fu) we kneel and bow. Where did this tradition come from?
Bowing in Kung-Fu will take various different forms; not surprising as there are hundreds, if not thousands, of individual styles from various families and various regions all throughout China.
In China, bowing (especially the traditional kowtow) serves as a sign of reverence. Modernly (following Imperialisms decline in China), the kowtow has been replaced by the standing bow in many formal situations. Bowing is also common under Buddhist traditions, especially when honoring both the student-teacher relationship, as well as in honoring ancestors and memories of predecessors.
Finally, bows may be used in apology. As @BenCole said in one of his comments to the original question, this may be a way of bearing the neck in a sign of supplication, but is commonly used by political and celebrity figures to show remorse for a perceived fault.
Bows in Chinese martial arts tend not to be as strict as bows in Japanese martial arts, as bowing is not such a formalized practice in China any longer. The core ties are, however, to both Buddhist and Confucian traditions.