At last I have found a reasonable PDF Reader on the iPod touch ..... and it was there all along .....
Unfortunately so far, all of the third-party PDF viewers for the iPod touch rather suck.
MobilePreview still in version 0.1 mentions reading pdfs as a "planned feature".
PDFViewer is too annoying to use, as it scales from the top-left of the document, not the centre of the screen and does not rotate.
The best solution I have found so far is to use MobileSafari, with the 'file://' patch applied.
I keep a folder of PDFs in ~/Media/PDF/ (which was where PDFViewer expected to find them), I copy them there using AppleFileProtocol, using AFPd (which also turns on Bonjour, nice).
MobileSafari is a far nicer PDF viewer than PDFViewer, but is less convenient because you cannot browse a directory.
What you can do though is to type in the URL to your PDF file, eg. file:///var/root/Media/PDF/TubeMap.pdf and when it loads, zoom into a representative part of the image and add it as a WebClip to your home screen.