What is your workflow for shooting timelapse?

I use Nuke as well. I shoot NEFs on my D700 and D7000, usually with three (D7000) to nine (D700) exposure brackets. I use aperture priority auto exposure for subjects with massively changing light or manual exposure for things with fairly consistent light.

I merge the NEFs using the batch mode of Photomatix (and HDR program that's quite inexpensive) into EXR files and then use these EXR sequences in Nuke.

For the auto exposure timelapses I use the Furnace Deflicker to smooth out the exposure (there's PLENTY of room in the EXRs to do this seamlessly). For the manual exposure no deflicker is usually necessary, though the Nikons' shutters do have some variability that sometimes introduces flicker, especially at fast shutter speeds.
 
One other note: If you are only shooting single RAWs there is no way to directly convert them to EXRs in Photomatix (it only works with brackets of 2 or more). It's a feature they removed from the current version, but they told me they would re-implement in the next update (due to popular demand). The workaraound is to duplicate the entire NEF sequence and batch process the images in pairs. Even though each pair of exposures is identical, Photomatix will process them as if they were brackets at a 0 stop interval.

You can also use Photoshop or Bridge to batch convert the NEFs to EXRs, but I much prefer the brackets and the simplicity of Photomatix.

Photomatix is a great purchase for stills work as well - well worth the $99
 
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