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ETA: I just popped over to the amazon associates site and see that they now have something called "context links" in beta. Is that what you're referring to? It would still have the same difference as stated above - for any payment from amazon, someone has to buy something.
An interesting thought after reading a few of the threads here about kontera and similar in-text advertisers. With amazon, you wouldn't have to worry about the company finding suitable advertisers for your pages (and they have a number of parameters you can set yourself). But I'd still rather link my own.
[edited by: Beagle at 11:16 pm (utc) on July 28, 2008]
I've never used kontera, so might be wrong on this, but my understanding is that it's pay-per-click advertising. OTOH, amazon is an affiliate program that pays a commission when someone buys something.
Personally, I find the pop up windows to be rather annoying, so I am removing them from my sites now.