The commonest site of Branchial cysts is -
Branchial cysts are characteristically found anterior and deep to the upper third of the sternocleidomastoid muscle. Branchial fistulas (those derived from 2nd branchial cleft) open externally in the lower third of necic, near the anterior border of sternocleidomastoid. Its internal orifice is located in the tonsillar fossa.
Branchial cysts & fistulas 

are remnants of the branchial apparatus present in fetal life.
branchial cysts, fistulas or sinuses are lined by squamous epithelium.
Upper 1/3rd of the SCM
Lower 1/3rd of the SCM
Upper 2/3rd of the SCM
Lower 2/3rd of the SCM