Going from NEF to JPEG between Adobe Camera Raw from CS3 (ACR,) Aperture (APR) and Capture NX (NX,) I see a pixel shifts, with NX and ACR being fairly close (probably a pixel difference,) and APR shifting things right a few more pixels. Doing white balance with each of the NEFs produced different results- though I may have been off in my WB point selection between images.
Contrast was different, likely due to ACR settings. Overall, I thought the NX JPEG was more "true" and the ACR JPEG was next. APR's rendering was disappointing compared to the other two, and I'll probably stop using it for JPEG conversion unless I can tweak the settings to make the results better.
Zooming in to 500% there were clear differences in details, though I'll have to play with sharpness settings to be confident of the results.
When I'm near a photo printer, I'll probably do a print-from-NEF test as well as test the TIFF converters of each program. This may change my workflow if I find I have to import to NX, then export out- I haven't checked Bibble Pro yet, but it's going to get tested too and then I'll figure out at what point I'm going to have to do wide angle lens correction.
Methodology:
I simply made three copies of the same NEF file, opened one in each converter, used a wall to set a white point, saved to maximum JPEG, then opened the JPEGs in Photoshop, turned two of them to layers and clicked on and off the view for each layer to compare them two at a time. Then I zoomed in to 100% and 500% and compared the details.