The Sharpening settings are as per ACR default.
That's your problem...the "Default" rendering is not optimized...you'll need to learn how to adjust the image in ACR to get the image quality you need. The idea is to adjust the sharpening parameters to get an optimal image at a 100% zoom in Camera Raw.
Are you aware that Adobe and other third party software does not read the in camera settings from you RAW file? The only in camera parameter that ACR and Lightroom use is the White Balance. Sharpening, Picture Control Profiles, Saturation, Contrast, Hue, Active D Lighting, and any others are ignored by ACR and Lightroom. When you open the RAW file in Nikon software all of these are read and applied to the rendering of the image. When you first open the RAW file in ACR or Lightroom, you get what is set as the default values for your camera. Unless you have set new defaults for your camera, sharpening is very low and probably not anything like you are getting from the camera and Nikon software. I don't know what Camera profiles are available in CS3 and ACR 4.x, but Camera matching profiles are avaialble in CS5 and ACR6.x that do a very good job of matching the Nikon Picture Control profiles. You need to determine the equivalent sharpening settings in ACR to match what you have set in the Nikon Software. You do need to have the image at 100% size in ACR to see effects of the sharpening.
Alamy requests that no sharpening is used, but people take this too literally and disable all sharpening in raw conversion, which is a bad idea. ACR defaults to Amount 25, radius 1.0, Detail 25, Masking 0 and Luminance 0; sharpening should also be fully turned on in preferences ("apply to" "all images", not "preview only"). You say you use defaults, but it's worth checking these things anyway, just in case.
I default to Amount 30, with Radius 0.9 and Detail 18. I've never had a photo rejected due to 'SOLD' (soft or lacking definition) because of conversion. You should also use an AdobeRGB workspace at 300dpi for Alamy. What you shouldn't do is use Workspace (output) sharpening, as that WILL get your photos rejected.
Thanks for the advice everyone; that seems to make sense. Once I have decided which settings to use, how do I save these as my defaults to be able to open images in batches?
Click the little fly-out menu icon at the upper-right and choose Save New Camera Raw Defaults.
But be careful, any setting you have changed from default will be saved, so you could inadvertently save a particular color balance setting (instead of As Shot) for example, and that wouldn't be good.
I am using CS3 and ACR 4.6; Some have suggested upgrading to CS5, however surely I shouldnt need to do this, as the Nikon D3 was brought out before I started using CS3, so it should work?
One thing I'd like to add that goes to this comment that you made in the original post: There's not just one result that can be made from a raw file. The quality of conversion results is continunuing to improve as Adobe refines their algorithms and more powerful computers are being built to run them.
The quality of conversions of the very same raw files from Photoshop CS5, using the PV2010 conversion process can indeed be superior to that from Photoshop CS3.
In turn, the quality of conversions from Photoshop CS6 can be better than that of conversions from Photoshop CS5.
We are seeing real improvements to this technology before our very eyes.
There's a hardly-noticeable menu icon avalable to the right of the tabs in Camera Raw, click on it and there is an option to "Save New Camera Raw Defualts". I start with an 'undeveloped photo', and only change what I think needs changing, before saving new defaults, then I click Cancel to return to Bridge. I also have the Camera Raw preference set to make settings specific to the camera serial number, so I can have different defaults for different cameras.