SATA will be better then PATA when HDD's get faster. Rite now, it's a bit of future proofing, along with the convenience of the smaller cables (no master/slave issues either). I've tried the exact same drives in this computer. One being SATA, and the other being PATA. They come out identical in the benchmarks. The point is that no single HDD can saturate the bus on either interface rite now.
If you're building a new machine, go with SATA, even if it's only for convenience at this point in time.
If you're building a new machine, go with SATA, even if it's only for convenience at this point in time.