Apple Store may be your best bet.
Have you tried importing some of the images Aperture fails to render into iPhoto? I believe you said you'd tried Preview but not sure it was on the same image(s). Aperture, iPhoto and Preview all use CoreImage to handle RAW conversion, although Aperture uses more elegant settings and fine tuning adjustments. However, at this level, either should show that the image is OK, or point at CoreImage being the culprit.
Other ideas to try to try and narrow the issue down:
Move your Aperture library / rename it.
Open Aperture which will create a new library
Set preferences to import as reference master
Import images (this will leave the images in their existing folder on your drive)
What do you get?
If the above shows pixelated images, then delete the project, reset the Preferences to import to Aperture managed library, and re-import. This will eliminate physical import to the library.
If the images are still pixelated, then go to the next test.
What happens if you import into PS CS2 / ACR and convert to PSD/TIF. Is the image OK?
If so, save as PSD/TIF (ensure Maximize compatibility is set to On or Ask in CS2 Preferences)
Also save a second version as a high quality (12) JPG
Import into Aperture as above, leaving files in their existing folder location.
What do you get?
If the above shows pixelated images as per NEF images, then we eliminate the RAW processing step.
Do you have access to another Mac running 10.4.8? Try the same thing on that computer (using your external HDD for the reference files).
You said your MBP has been playing up over the last few days. How so, and in general or only with Aperture?
G.