My all time favourite is Nike every new website that they release is beautifully designed. With the use of imagery and animation they capture the essence of Nike even before they display one of their products. There are thousands of examples out there, I think its time for people to put their negative opinions of flash behind them and see it for what it is.
I guess it all comes down to one thing; use it wisely and it will enhance the users experience. Oh and don't believe everything you read Jakob Nielsen may have done a lot of good for usability online but he has also influenced many people to follow unnecessary constraints.
Other articles of interest : Macromedia’s Top 10 usability tips for flash web sites
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