For SEO, is a 301 or 302 redirect better for affiliate links?
Are there any benefits/drawbacks for either?
PriceGrabber uses 301
Shopzilla uses 302
Nextag uses 302
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Either will put the user at the destination - the redirect status should not make any difference unless you plan to change the outgoing link target associated with the redirect key (in which case the 302 Redirect is the better choice, as clients' browsers will ask your server for the new destination on subsequent requests instead of caching it).
What about SEO reasons?
Your outbound link script should be blocked using the robots.txt exclusion protocol - unless you want to experiment.
I can't imagine any potential benefit to telling the search engines that some of your site's internal links are intended to be links to other sites - maybe it will count toward the ranking of those affiliate target pages?