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Is there favorable treatment from an SEO perspective if you use Google Checkout?

No, but they show an icon in AdWords and Google Products One Box results next to stores that take Checkout. Any trust indicator like that usually helps.

It may increase your chances of appearing in the One Box as well (as opposed to simply determining whether you get an icon next to your name), but I haven't heard that definitively.

That would be highly unlikely in organic search results.

there is speculation that google could use checkout to track conversions

imagine the power of tracking a customer from ad click all the way through to checkout

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