Having, say, IIS as the web server for your intranet is not a hindrance for having Vaadin applications for intranet use anymore. Vaadin XS makes it easy and fast to add Vaadin applications anywhere in your DOM. You could think of it as adding portlets without a portal application server.
Embedding Vaadin applications has previously been possible with iframes, but that has some technical limitations: Security related issues, communication with the "host page", and resizing the content with iframes can be tricky at times.
On the tech specs side of things, you only need one servlet container to serve your Vaadin application(s). But, as already mentioned, where you display the applications is up to you, on top of any server and technology you want. Apache, IIS, ngnix; PHP, Django, Ruby on Rails, static HTML pages &em; there's no limit.
Matti's write-up explains the abstract and the concrete, so go ahead and read it from our wiki: Hosting Vaadin App on Remote Server.