I have small html pages that just redirect with the meta refresh code to affiliate urls, this i do for tracking the clicks to my affiliate links better, is this seen bad by search engines? Should I instead drop those redirects and use the normal aff. links?
You should be fine. As long as the rest of the links on your site are more normal, it really wouldn't affect your rankings too much. You can always test and find out how it personally affects you though.