Highlights that you thought were unusable are easily rescued with Lightroom 4.
These three images are all from the same base image that I was going to use as part of a set of 5 for HDR because of problems with highlights.
The three images are - "from_camera.jpg" (this is the image imported into Lightroom, without any adjustments being applied). "lightroom_process_2010.jpg" is the best I could get with Lightroom v3.6. Maybe I could make it a bit better but going further requires messing around with tone curves and is quite tricky. Lastly, "lightroom_process_2012.jpg" is what I get with Lightroom 4.2
Of the three, it is the one from Lightroom 4.2 that looks the most natural and as can easily be seen, a lot of detail is recovered from the clouds whilst a little bit of saturation fills out the colours with some body.