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It all depends on whether you feed search engines different content than you serve to human visitors, and to some extent, the motivation that causes you to do so.
The test you have to pass is this: If a competitor reports you for trying to fool the search engines, will your site pass inspection? This line can be fuzzy, and it is best to stay well inside the safe area!
For Flash, I think the best approach is to put up alternate non-Flash pages, and offer them to your visitors who prefer not to see Flash. When a spider comes along, just redirect it to the non-Flash pages. Here, the spider sees exactly what a human would see, and there is no intent to "fool" the spider.
I hope I understood your question. The above is my opinion - it is worth what it cost you... :)