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Another possibility is to use a script that cloaks your affiliate code. Instead of some unwieldly url, it will just appear as a regular domain name. I don't know if they are frowned upon by the search engines (or if it even makes any difference at all), but I have heard of some affiliates using scripts like these.
[edited by: CatLady at 2:40 am (utc) on Oct. 2, 2007]