Will Google see site.com and site.com/?partner=123 as two independent sites or as the same site? If they are considered two independent sites, I guess it will give problems with duplicate content if they have the same content?
Consider its the same domain, yes it is considered the same site. Sub-domains are consider different to a point.
I know that google has gotten very good at canonical issues. If http://site(dot)com, http://www(dot)site(dot)com, http://www(dot)site(dot)com/index.html, http://www(dot)site(dot)com/default.html, etc. all pull up the same page then links to them will now be counted as links to the one of them that google considers the main page, so I guess that if site(dot)com/?partner=123 just pulls up the same page as typing in site(dot)com then the links will all count towards site(dot)com although google might be getting smart at recognizing affiliate links and discounting them compared to links they consider as editorial votes
Yes but since it says partner it is likely to be a refferal link so if you join from it the person that posted that link will probably get paid for it.
Okay, so site.com and site.com/index.php?partner=123 will also be considered the same? Then we don't have to do anything to avoid duplicate content?
What you're really asking is whether site.com/page.php and site.com/page.php?arg=whatever are the same page? A site is typically defined at the domain level, so site.com/abc.html and site.com/folder/zyx.php are both part of the same site. The same physical page with different query string arguments seem to be treated as different pages. A lot of blogs use the default id=x permalink structure....
So if site.com/page.php and site.com/page.php?arg=whatever are showing the same content, I might get in trouble for duplicate content? How do I avoid this problem?