What I'm using is haXe and swfmill, plus some custom Python utility scripts. swfmill can compile assets into a .swf, and the haXe code can be compiled into that .swf afterwards. You can use FlashDevelop for an IDE - it supports haXe out of the box.

You can also use Actionscript (take a look at the Flex SDK) with FlashDevelop, and I think there are other options as well, but I haven't investigated anything else so far.