<p>I think the best part of flash is the possibility to create not squared user interfaces, so I like the idea to create desktop apps using flash. I know AIR is for that but it doesn't allow real access to OperatingSystem apis and dlls and the commercial options are kind of difficult to customize.</p>

You can try ScreenweaverHX:
http://haxe.org/com/libs/swhx
It's the Haxe-based successor of the old Screenweaver. However, it's not as simple as the old version used to be. Most likely you need to take a look to the basics of Haxe and Neko, the 2 technologies it's based on.
There's another project on top of SWHX that it's called HippoHX. It aims to "complete" SWHX providing that extra functionality you might miss (simple ActionScript APIs and a GUI). However, it's in its early stages:
http://hippohx.com
DISCLAIMER: I'm the owner of HippoHX, so my point is obviously biased.
As far as I know SWHX is the only Open Source alternative at this point.