Hi Cactusgod,
Firstly I don't have a PRS-600, only a PRS-505 but I think these experiences with putting PDFs on the reader are probably fairly typical.
The good news - if you use Calibre to convert your PDF to EPUB or LRF then you shouldn't get the "too small to read" problem because calibre allows you to manipulate font-size. The "too small" thing happens when you transfer the PDF to the reader directly as a PDF and is because there is so much useless "whitespace" surrounding the text that the bit you're interested in is squashed into the middle. You can use the magnifier button to make it bigger but you risk losing images and formatting when you do. Also don't forget that on a Sony you can make the text bigger by turning your book through 90deg and reading in Landscape format.
The bad news - although Calibre does a very creditable job in converting PDF to EPUB/LRF (via HTML) it's not perfect. I don't think the perfect converter exists yet. The sort of things which can go wrong are:-
PDF headers/footers/page numbers end up mixed in with your main text. Calibre provides a facility to remove these using Regular Expressions. So if you are skilled with these you will get better results. If you're not you will have a bit of a learning curve as they're a bit of a "dark art".
Images and hyperlinks can go missing
Detailed formatting e.g. Centre, Right align may be lost
Paragraphs are not necessarily reconstructed correctly from their constituent lines
How much you care about any of the above is very individual. Some people don't give a toss about formatting as long as all the words come out in the right order. Other people get hung up if there's a quotation mark missing! It's probably fair to say that those people who are trying to read highly formatted technical documents with hyperlinks, e.g. IT manuals, are less satisfied with PDF conversions than those who are trying to read the latest whodunnit novel.
There is more good news. I know that improving PDF conversion is high on the list of priorities of the Calibre developers - so things can only get better. Also you can try pre-processing your PDF with one of the free utilities around which attempt to remove the useless whitespace from the PDF before you transfer it directly to the reader. I've had some success with soPDF, but it didn't work with all my PDFs.
I, personally, prefer to convert my PDF novels to MSWord and beat them into shape with my own utilities. But I have to be careful not to spoil the plot by reading things at the end of the book I'd rather not have seen!
In summary, if you have 100 PDFs you'll probably need about 98 different ways to deal with them. However, I would advise you stop dilly-dallying and get your new reader. They're fantastic. Just think how much more room you'll have in the house once you can give away all your old p-books!