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Are there any known security issues related to running a web application via a .hta file. I am especially interested in the drag & drop issues related to .hta files and frames

see: http://sqlblogcasts.com/blogs/jonsayce/archive/2008/01/10/drag-and-drop-problems-in-hta-frames.aspx

+1  A: 

I guess it depends on whether you mean current (unpatched) vulnerabilities, or vulnerabilities since HTML Applications were first introduced? See this Google search for examples of the latter. You should also check if HTAs are still going to be supported in future versions of Windows/IE.

BrianLy