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If it is the case that no URL for .us should exist (there are not new URLs) then you can remove pretty swiftly in Webmaster Tools >> Google Index >> Remove URLs >> select the root URL and select to remove all directories that come from it.

Rel=canonical is great for helping search engines serve the correct language or regional URL to searchers, but I'm not sure how it would work for two sites both purposed for the US (.us and .com). What's the thought behind having two sites - is the .us site intended for Google US searches and .com the default for anything outside of the US? Are there language variations? What are the different "locations" you're referring to?

Since the onclick event is a Javascript issue it's to all intents and purposes ignored by the search engines. What counts is whether or not your link appears in the href attribute, and whether or not the link is nofollowed. If you do not have it set to nofollow, there is a slight chance they would follow it, but as stated above, Google is pretty good about parsing javascript links.