I'm currently going through the SharePoint Planning and Architecture documentation, planning a SharePoint installation. I'm on the section "Determine Sites and Subsites".
One of the things suggested to take into account for each site is what site template you will base it on. A number of the sites on our site will be existing ASP.NET applications that we're embedding into the new SharePoint portal -- I'm wondering in this case, is the thing to do to base the site on the "Blank" template?
It seems like the obvious option, but I'm not entirely sure of the best procedures to follow when embedding an existing application.
EDIT: just to provide more information, one of the embedded applications would be, for example, our own custom-built issue tracking/support system that we've used for a while. I would simply envisage us having a link on either our global navigation, or the current navigation (the vetical menu on the left..), which when clicked upon brings up the issue tracker application within the same master page/branding layout that everything else on the SharePoint site is displayed within.