I would like to know if it is best practice to store adsense codes in external javascript files. Do you guys out there store yours externally or can they be viewed with 'view source'?
You can do that. I you store it in a .js file and load it, then it is transparent to google. But if you store in .html etc and load it thru iframe/frame then you need to select 'frame-enabled' code from google.