iPad + iPhone

Yahoo.com (note: email and instant messenger)

ESPN - nice top score ticker and sliding animation on the iPad video carousel, polls are part of the large scrollview which encourages user participation

CNN.com

nissan.co.uk

sevnthsin.com/new/iphone/
- though its difficult to read the label when using your thumb

subaru.com
- includes roadside assistance which isn’t highlighted on the desktop site

Sistine Chapel VR tour

iPhone only

soundcloud.com
- an in-browser audio player that doesn’t have to be in the foreground

Basecamp

Financial Times - when you browse to it on the web they promote for you to switch to the “new FT app” with “no need to download.” It prompts you to increase database size to 50MB, clippings lists for signed in users, nice top menu

Forbes

Major League Baseball

TravelTex

Best Buy
- uses your location to provide the weekly ad

nikerunning.nike.com

dropbox.com

npr.org
- they got away from simple links like nytimes. trend towards tappable over clickable interfaces

gilt.com

huffingtonpost.com

yelp.com - nicely app-like, quite different from both desktop web and native app, but cleanly laid out for the phone, plus geolocation

Disney (iPad shows phone version),

Wikipedia - alternate phone layout, with some sections initially collapsed

Resources:
http://www.webbyawards.com/webbys/current.php?media_id=127&season=15
scoutzie.com
dribbble.com