The best replacement for web application is website.

The best alternatives to web application are rated as following:
★★★★★  website
★★★★★  desktop application
★★★★  web service
★★★★  windows application
★★★  web site
★★★  site collection
★★  web project
★  virtual directory
★  mobile application
★  website project
★  client server application
★  enterprise application
★  standalone
★  application software
★  web forms application
  client server
  software application
  web page
  standalone application
  windows forms application
  portal
  website visual studio 2010
  non web based application
  website .net
  site collection sharepoint
  web site asp.net

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Google Trends

Scale is based on the average worldwide traffic of web application in all years. Click on graph for more.
web application
website
desktop application