You can't run IE6 on a modern version of Windows. You can run it in a VM, which is Microsoft's "approved" approach (they provide old version of browsers for this kind of thing)
Most people don't understand the "old IE6 app" issue - it actually applies to a very, very small number of apps. It isn't that these apps don't display in other browsers because of bad HTML - it is because they use weird IE6 only technologies. Microsoft came up with some very strange things over the years (look at Data Islands: http://msdn.microsoft.com/en-us/library/windows/desktop/ms76...), and fixing these apps isn't just HTML tweaking. Of course, if you still have a Data Island app around these days your IT department should be fired...
Most people don't understand the "old IE6 app" issue - it actually applies to a very, very small number of apps. It isn't that these apps don't display in other browsers because of bad HTML - it is because they use weird IE6 only technologies. Microsoft came up with some very strange things over the years (look at Data Islands: http://msdn.microsoft.com/en-us/library/windows/desktop/ms76...), and fixing these apps isn't just HTML tweaking. Of course, if you still have a Data Island app around these days your IT department should be fired...