I have probably about 15'ish affiliate links on the homepage of my website, and I don't want those links to be taking away from the Page rank given to the other external links on my homepage. Would adding a rel=nofollow to the links fix this problem, or will I have to change the link to mysite.com/redirect-to-affiliate-link/ and redirect that link to the affiliate link?
I would have put a script in a seperate directory and do URL redirecting. Then, disallow this script dir with robots.txt
If a SE ignores rel="nofollow" what makes you think they will adhere to robots.txt? Both have the same effect and rel="nofollow" is a lot easier to implement.