A portion of our site is done in PHP and a portion of our site is done in ASP.Net. We just set up a new web server with Windows Server 2008 R2 which has IIS 7.5 installed.
I understand that IIS 7+ supports PHP, but can PHP and ASP.Net run side-by-side within a single web site in IIS, or would I have to set up one web site for the PHP pages and one web site for the ASP.Net pages?
You should be able to run both in the same site, but be sure that the AppPool for the site runs a "classic" ASP.NET pool configuration. The default AppPool routes everything through ASP.NET, and you won't want that for your PHP pages.
Other than that, you should be fine. Query strings, files, and back-end databases will be the best way to share data between pages.