Let's say I have the same TeX input, do different TeX distributions produce different PDF, and if so, which would produce best quality for print? I know my Miktex uses fontconfig to some intent, would a Mac OS X TeX distribution use Quartz/Cairo font facilities for instance?
No. All free distributions of TeX software (i.e. MikTeX & TeXLive) use the same software which produces the same results on all platforms.
Note that this may not be true for the few commercial distributions left (e.g. BaKoMaTeX).
Martin Schröder's answer is entirely correct. The different free distributions use the same software and so should produce the same results.
However, different versions of pdfTeX may produce different PDFs. This is not necessarily a matter of quality, though, and I doubt it would make much difference to the printed result. It might, however, make a difference to the size of the PDF, for example, or to its compatibility with different PDF viewers. That said, the defaults are very conservative so it is very unlikely a PDF produced by even the latest pdfTeX will not work on the vast majority of machines. In fact, this has happened to me only once on a campus which was using a really ancient version of Adobe Reader. The PDFs produced by default by pdfTeX at that time could not be viewed on the standard PCs. The PDFs produced by a sufficiently ancient version of pdfTeX would possibly have been OK. (Since it is easy to alter the version of PDF produced, I didn't pursue this line of enquiry.)
Print quality would be affected if fonts were not embedded and the document was printed on a machine which did not have fonts matching those on the machine where it was produced or which had different versions of those fonts. Again, though, all reasonably recent distributions have embedded all fonts by default, including the base 14 subset of the 35 postscript fonts (for documents using scripts which are not too large e.g. Latin, Greek etc.).
Different results might also be obtained on a machine where the local administrator had changed the default settings system-wide e.g. to use a different set of the 35 postscript fonts or to embed or not embed certain fonts. But that is not a question of the distribution of TeX in use but of the way the distribution is customised for the local environment.