My experience is that the noise reduction plug-ins like Neat-Image, NoiseNinja, etc. are significantly better than NR in ACR 5.x. The marketing material about LR-3 (ACR-6) touts that NR is better, that my limited experience with the LR-3-beta is that its NR is stll underwhelming.
My budget is limited ... it stung to spend big bucks on CS4, then about $70 on Neat Image 6.1 because ACR 5.x NR was, IMO, inadequate.
I'm not an ACR/CS4 expert, but my impression with high ISO pictures is that you want to do sharpening near the end of the workflow, especially after NR. I would like to use the much improved sharpening (and Clarity) that is available in ACR 5.x, but that detracts from the effectiveness of the NR plug-in, especially for high-ISO pictures. It doesn't seem to matter that much with low-ISO DSLR images.
I would appreciate the Adobe PS team working with the the NR plug-in vendors to give them a "hook" into the ACR pipeline. Their plug-in would be invoked by the ACR "engine" at the appropriate point in the pipeline, perhaps very early even before White-Balance and exposure/brighness/contrast adjustments.
In a batch of "sync-all", my impression is that you want NR to act on the "raw - raw" image before any exposure or contrast adjustments. When you increase exposure for an underexposed image, the shadows becomre noiser, and this can throw off pre-built noise profiles (as least that is my experience with Neat-Image 6.1).
My preference is to do as much of the Post-Processing as possible in ACR for images that don't need layers. That way I can minimize use of PS when appropriate. At this time, I find myselft invoking PS for all images to do NR.
But perhaps I'm mis-informed (wouldnt' be be first or last). I've had email correspondence with the Neat-Image support person (also may the be developer?), and my understanding is that such as "hook" isn't available.
Of course, the really preferred suggestion would be for ACR to have as good or better NR as the plug-ins, but until then, it would be appreciated for Adobe CS4 to be more "plug-in friendly".