You either need to store the PDFs as email attachments, save them to something like box.net to view using the browser, or else jailbreak your phone and use the PDFViewer software, but these are relatively easy...
Sounds like a pain in the proverbial to me. I hope Apple sort this out soon as I would really like an iPod Touch.
FoxItReader is worth checking out for Windows and WindowsMobile. As is PocketXpdf for Windows Mobile.
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