It's a great question. I wonder how many companies that are into "Flash" even have a clue about SEO. Sometimes I think there are two basic approaches to the web. One is the "gizmo" approach, and the other is the marketer's approach
Here are two exceptional cases I researched on IXQuick -- somehow some these companies got good ranking with a Flash site.
The LCD projector company, InFocus [infocus.com] has a very tastefully done site -- the Flash really enhances their message and the navigation experience.
Their index page is number 2 on Fast and number 4 on Excite for the kw "projectors". I can see no evidence of any attempt to optimize the page at all -- no meta tags, no text at all-- but there are the positions.
A second case is MacroMedia (the creators of Flash) who have a number 5 page [macromedia.com] on MSN for "vector graphics". The phrase is nowhere on the page or in the code! What's more, URL is both Flash and frames.
I think that Flash is too good visually and too economic in file-size just to go away. When used judiciously, and not for a bombastic epic movie, I'll bet that SEO can be done successfully. I will probably be trying such an effort in a few months.