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Regarding Google you don't have to worry. Google values content and related links.
There's a forum here on Webmasterworld that covers affiliate programs. That would probably be a good place to pick up additional tips.
My advice: It's not just a matter of slapping up a banner. Finding the right program and presenting it in the right way can make a HUGE difference, seriously. I can run two affiliate links on the same page and see a hundredfold difference in earned revenue. So never stop testing.