Some time ago I heard that having affiliate type links on the site like from the major affiliate programs can hurt site rankings.

Is this true and if I place a link or so on the site will Google pick up on this and recalculate rankings? If placed, is it better that the link be html or javascript for this reason?
Already I have had Adsense for content on the page in question that I will remove (which is being used with a tracking page).

Doesn't Google try to stipulate that their Adsense not be used with other targeted advertising on the same page? (legal?)

Affiliate links in and of themselves are no problem. If they were, the many folks making money as performance marketers would be out of business.

What search engines -- and not just Google -- don't like are what is referred to as "thin affiliates", those that do not add any other value to those affiliate links. Crafting your own, original content is the best way around the affiliate link stigma.

There is no prohibition to using AdSense on the same page as affiliate material. In fact, if done correctly they can nicely coexist and complement each other.

I think this topic has been covered before somewhere, but either way I'll throw in my two cents in case it's lost in the depths of the forum somewhere!