You sure can, there's a lot of information on the site about integrating YAF with an existing application.
I'm working on starting up a YAF centered site, and a "Master Page" kinda sounds like something that I have in mind. But I can't say that I envision it being "an existing application" other than the fact that I expect it to be in asp.
What I have in mind is basically a page that looks more like homepage of the website rather than an index of the forums. I'll have various cells placed around that will contain links to news articles, user stats, newest user data, common links, and other relevant information. One of those cells would also have a condensed view of the forum, maybe showing the latest 5 (or 5 most active) posts within each of the subforums... Obviously, this homepage would use the same styles & themes that the actual forum uses so that it's a seamless transition for the users.
Here's a link to a screenshot of something for phpBB that's sorta like what I'm talking about.
http://www.evolution-rpg.com/Image2.jpg Are there any applications or plug ins for YAF out there that kinda fit this description? If I just had a few names to search on I think I could work out the rest on my own..