i have a php page that grabs an id from a query string and directs to the appropriate link. for example link.php?id=page1 If i block the link.php from being indexed inside my robots.txt file will this effectively stop those links from passing juice to the affiliate site? Thanks.
It should do, yes. Basically you are telling the search engines not to bother indexing those links, and if they don't follow them then they can't be assigned a pagerank (or whatever Yahoo and MSN use).