We're currently working on a major overhaul for our public website, transitioning from a pretty nasty static site to a new CMS. For some reason or another, Joomla was selected as the CMS despite the company being a very heavy MS shop. This would be fine, however we have multiple ASP.NET web applications which are currently running on the site, which need to be integrated seemlessly into the site. The migration itself has been outsourced to a local company, who are moving all the static data over to Joomla (a huge job), as well as offering the Joomla installation (as part of their web solution).
One of the key reasons I really wanted a web upgrade at all was to ditch the frames based approach used in the older static website, so that users could bookmark search results or records from the ASP.NET applications.
The problem now lies in Joomla being PHP based, so integrating our .NET apps is hardly a walk in the park. It seems the company who was outsourced to do the CMS migration is happy to simply place the .NET stuff in an iframe and leave it at that, however I find this unacceptable; mainly due to the bookmarking issue.
Are there any nicer ways to do this integration?
Edit:
As per jlleblanc's answer, the .NET applications are specific independant sections of the site. There is no need for integration on a global scale across the site. I had considered your suggestion of mimicking the Joomla template; this could possibly be the approach we take.