what are the "biggest" (performance) differences using PD on windoze or linux i'm (at the moment) mostly interest on audio analyzing and visual creating (GEM)
this largely depends on your sound card, linux is able to get increadably low latencies (under 1ms in the kernel) and is of course much more stable. Miller has added some support ASIO drivers in .35 which means, if your soundcard _has_ ASIO drivers, pretty darned low latencies for windows as well.
Josh .. Yoshi .. Joschi .. xiphoidprocess.com .. eds.org/~joschi