I don't know if they were the first but I think of 37signals and Basecamp as the ones that first nailed the multi-column/highlighted plan form of design that has become so dominant.

Here's 2009: https://web.archive.org/web/20090307125843/http://www.baseca...

if you go back to 2007 you can see the same structure in a plainer presentation; it's easy to see how they went from one to the other: https://web.archive.org/web/20070831191822/http://www.baseca...

Pretty interesting!