I have basically two separate sites, a SharePoint collaboration site, and an ASP.Net application site. The only linkage between the two are the hyperlinks going back and forth, and the user validation on the behalf of the SharePoint site. The user will enter and be authenticated through the SharePoint site and then may browse to the ASP.Net application.
What is the best way to integrate the two sites together? Is there an easy way to give the users a seamless experience while maintaining two sites?
UPDATE: I followed all of your advice and settled on going with Chris' answer.
Andrew Connel actually deploys the .aspx code behind pages as a SharePoint feature.
He sets out how to do this on his site here.