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I can't help you with embedding Flash, but I can give you this advice about getting pages to open in a new window:

Add the attribute target="_blank" to the end of the attributes list for your anchor tag. For example:

Code:
<a href="blah://bogus.page/" target="_blank">Bogus Link</a>

However, you can do nothing to override browser settings, such as Firefox's setting to force links that open new windows to open a new tab instead.
 
iWeb Enhancer will let you add flash content to an iWeb site. (Link)

I've never used iWeb Enhancer, not exactly sure how it works, so use at your own risk.
 
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