Performance-wise there isn't that much of a difference for equivalent models, but you have to keep in mind that PATA (standard old ATA) will probably a thing of the past in a few years, some motherboards are now equiped with only a single PATA port (probably just because CD/DVD are rarely SATA). Therefore, if you buy a PATA HDD now, you might not be able to fit it in a future upgraded system.
The other thing is that the most recently introduced HDD are generaly a bit more performant than old ones and sometimes are exclusively available in SATA.
That is pretty much the only reasons I would go one way or another.