These sites are not in any particular order, and fresh off of the Interactive Telecommunications Program Alumni list.

http://www.apple.com/html5 (examples of html5 sites)
http://developer.apple.com/safaridemos/ (more demos)
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http://www.20thingsilearned.com/en-US
http://www.nikebetterworld.com/ (like the pagination on the side)
http://www.newzealand.com/us/
http://siteinspire.com/ (job site)
http://www.googleartproject.com/
http://www.good.is/
http://www.subtraction.com/
http://www.yourauxiliary.com/
http://cssremix.com/
http://www.cnn.com/ (no ad banners, only in-house promotions)
http://meandoli.com/ (flash site)
http://www.moma.org/explore/collection/ge/index
http://www.moma.org/interactives/exhibitions/yap/
http://www.moma.org/explore/publications/modern_women
http://chrisglass.com/
http://www.aaronkoblin.com/
http://www.huongngo.com/
http://vectormill.com/
http://www.cascadebreweryco.com.au/
http://interactionhero.com/
http://www.conversationsearth.org/
http://the-planet-zero.com/ (View in Firefox)
http://www.monet2010.com/ (View in Firefox)
http://www.freescreencleaner.com/ (View in Firefox)
http://www.makr.com/
http://spacelog.org/
http://nyan.cat/
http://www.projectnoah.org/
http://ericandre.com/
http://css-tricks.com/ (nice flexible layout)
Funniest site that break rules:
http://yvettesbridalformal.com/