According to A Dictionary of English Surnames by Reaney & Wilson, Annakin is a surname from Yorkshire, England, that goes back to the Norman French name Anketin, itself a form of the Old Norse name Askell or Asketill, "divine cauldron".
While we know the origin is from a friend of George Lucas', it should also be noted that there was once a group of people the Jews defeated named the "Anakim" or "Anakims." These people were referred to as giants. (Deuteronomy 2:10-11 – "10. The Emims dwelt therein in times past, a people great, and many, and tall, as the Anakims; 11. Which also were accounted giants, as the Anakims; but the Moabites call them Emims.") Ironically, Anakin Skywalker (or Darth Vader) from Star Wars was also referred to as a giant of a man in many of the books. Therefore, the name could be used to mean a giant-like or generally tall person.
Nicknames with the suffix -kin seems to have been used in medieval English (at least according to this site). Wilkin was a nickname for William, Hopkin was a nickname for Hob (Robert), Larkin was a nickname for Lawrence, etc. So I guess Anakin (well, Annakin) could have been a nickname for something in medieval English. A diminutive of Andrew, perhaps?