I am a detractor of Flash for quite a few reasons (positioning, usability, CPU consumption ...) but I have to admit that real wonders can be done if it is put to good and creative use.
After the jump there are quite a few websites that have made really good use of Adobe technology to make very interesting, creative and intuitive websites. And is that if Flash is still the preferred by many brands for their sites, it will be for something.
Source | HongKiat 
The 3rd Generation Prius
Galaxy tag
Tag Galaxy is a very good flash application that uses Papervision3D with beautiful transition effects to explore Flickr photos via virtual planetary systems. You enter a tag and related tags appear with beautiful planetary systems. 
Mercedes Benz | B Class
The CLUE Virtual Mansion
Flash 3D game. Beautifully made. 
If Your Milk Carton MoOOos, You Win!
Case-Mate: I Make My Case
You can design your custom iPhone case in this cool Flash application. 
PlateInteractive
Creative idea with fantastic effects. 
SposiAmo
Wedding planner site from Italy. Elegant design with romantic music background. 
DG Stylists
Cheese & Burger Society
GT3 Creative
Skoda Yeti - Catch and Win!
Lois Jeans | SPRING SUMMER '09
Harajuku
Christmas Tweets
IKEA Soft Toys AID
infrared5
Pearl jam ten game
Stefan Kovac - Portfolio
Flash presentation of Stefan Kovac's selected web & interactive work. 
The Scruffs game - unofficial site
Herbal Essences Spice
Beautiful graphic design, and nice animations. The website also has games. 
TheOleg | freelance designer
This is the site of Ukrainian freelance designer Oleg Kostyuk. 
Daniel Kosaka
Interactive Design Portfolio of Daniel Kusaka from Brazil. Interesting design. 
Wonderful Moment Project
Volkswagen Efficiency: Volkswagen UK
PIAGGIO MP3
kasulo.ws
Portfolio of Ricardo Dias featuring web and print contents. Gorgeous design, and inspiring idea. 
lech.pl
MILK beer in 3D 
Pritt - Knutselwereld
GOOD | How do we achieve harmony?
Verbatim Championship
Cool robots with cute animation. 
McCafe / Make Your Own Cappuccino Art
You can make your own cappuccino art and save to gallery. McCafe from McDonald's. 
HBO Imagine
TESTEMALE-PHOTOS.COM
Bernard Testemale's professional photography portfolio site. 
Levi's® 501® 2007
THE PROFILER ™
Use The Profiler to visualize what's behind your profile picture, and discover what goes on in your friends' heads. You can connect with your facebook. 
Red Bull Soapbox Racer
Red Bull Soapbox Racer is a 3D racing game in Flash. 
Toyota: Every 5 seconds
Featuring Toyota cars: Yaris, Auris, Corolla, Avensis, Camry, RAV4, Prado. 
hiroshi seo / photographs TIME: LINE
Hiroshi Seo is a photographer from Japan. 
Beautiful examples of websites made in Flash. That they are a good option for brands so recognized that more than positioning they are online to screen fans who have earned them based on good products.
Thank you for sharing them! It would not be bad to look around, which ones do a good integration of html and flash to take advantage of the best of both;)