On past projects I have made web parts collapsible by wrapping web part zones with code in the page layout. The disadvantage with this approach is that it is not adjustable by the client without modifying the page layout. A project I just wrapped up required the flexibility for site owners to add or remove web parts that automatically became collapsible. This project was for SharePoint 2010, but I converted the solution to work with SharePoint 2007

Applications, computers, file shares all utilize AD for permissions for starters. AD when it comes to SharePoint it can be looked at in two parts. The user and the security group.