Can I get a list of all urls on my site from the Google Analytics API?
I have a site www.domain.com and wanted to get all of the urls from my
  entire website and how many times they have been clicked on

I guess you need parameter Page and metric Pageviews

I am especially interested in some of my external links

You can get list of external links if you track they as events. 
Try to use some crawler, for example Screaming Frog. It allows to get internal and external links. Free use up to 500 pages.
I have a site www.domain.com and wanted to get all of the urls from my entire website and how many times they have been clicked on, from the Google Analytics API. 
I am especially interested in some of my external links (the ones that don't have www.mydomain.com). I will then match this against all of the links on my site (I somehow need to get these from somewhere so may scrape my own site).
I am using Python and wanted to do this programmatically. Does anyone know how to do this?