Nr. 1: flickr
Nr. 2: Google Docs and Spreadsheets
Nr. 3: Line Rider
Many thanks to all who participated in the survey!
Sidenote: I’ve originally asked only for betas which launched in 2006, but since most submitted lists contained older sites as well I kept them in using 0.5 pts for apps from 2005 and 0.33 pts for apps from 2004.