I'm in the process of figuring out what works for me, but for now it's by hand for sure. Did my first round using Sublime Text 2, but have just switched to Coda as I can open a preview pane below my code that auto-refreshes every time I edit the CSS which means no window or app switching to refresh.
I had tried previewing in Dreamweaver which I usually use for coding (but never the wysiwyg features at all) and that was a disaster. What a goddamned mess Adobe's software always is, so if this forces me to get friendly with Coda and move away from DW then great. Haven't messed with Edge Animate as I was guessing it was also going to be a mess. Haven't touched GWD or Tumult Hype (another app option I haven't seen mentioned here, no idea how flexible it is).
Currently using CSS Hat (see above comment) to grab CSS in Photoshop for bits of the design. Now looking for something that will output the basic HTML markup to save one more step and at least have some basic markup to start with. Not sure exactly how that would work efficiently enough to save time but looks like there are a few tools out there that might be worth a look.
For now though it looks like Coda, GSAP, & CSS Hat will get me most of the way there.
I tried Swiffy to convert a SWF and was fairly impressed with the results, but even Google says that it's a temporary solution, so I wouldn't expect that to stick around in the long term.