Check out CNET's 'WebWare 100' award winners, even though the list isn't very distinctive in that it contains just about all the usual suspects.
Notable absentees include many of the big virtual reality sites (Second Life et al). Only the MMORPG Gaia made it to the list.
Other sites conspicuously missing include NYT's About.com and Yahoo! Answers; mash-up engine Yahoo! Pipes; social shopping sites like Shopstyle.com; office suite look-alikes such as Zoho; social address book Plaxo; video (and revenue) sharing site Revver; blog search Technorati.
In the 'Productivity and Commerce' section my eye fell on Basecamp (project management tool from 37signals).
I counted 13 apps from Google, 9 from Yahoo!, 8 from Microsoft, 5 from eBay and 2 each from Amazon.com and News Corp. Taken together, that is just a third!
For reference: read this CNN Money article on virtual reality; Time.com's article on 37signals, belonging to a category that looks like a new area for telco's to go takeover shopping; this survey from Evans Data, ranking Web 2.0 developer programs (do not go beyond page 28 for text errors).