SATA-2 64MB cache or SATA-3 32MB?

I was going to write an answer saying if speed for transfer was important for the large backup files then use SATA-3, but after looking at this paper http://www.seagate.com/docs/pdf/evolution_to_sata_6gb_storage.pdf I'm not sure if the interface speed is going to make a difference, because it is the hard drive that is the limit.

Why Is SATA 6Gb/s Needed Now?
Today, hard drives for PCs don’t seem to be pushing the limits of the SATA 3Gb/s interface. The highest-performance desktop drives on the market deliver about 1.5Gb/s in sustained data transfer rates. Add another 0.5Gb/s in command overhead that is not available for general data transfers, and you still have 1Gb/s of headroom before you bump into the 3Gb/s ceiling. But it won’t be long before hard drive technology catches up to the SATA 2.0 standard. Seagate estimates that hard drive transfer rates will exceed 2.5Gb/s by mid-2011. Add in the 0.5Gb/s command overhead, and the SATA 2.0 standard is out of gas.

The PDF was dated January 2010.

The did do a comparison between SATA-2 & SATA-3, and 32MB & 64MB, but unfortunately, they compared slow interface and less cache to faster interface and larger cache. It would have been interesting if they did the comparison you were looking for.

Unfortunately, I think looking at the hardware websites and getting independent numbers on the actual throughput is the only true way to know.

I'd go with the larger cache. The speed difference is only for bursts, and iirc it's a number your disk will rarely reach. Being able to keep more data cached should help a lot more.

But why choose? You can have both for only $70:
http://www.newegg.com/Product/Product.aspx?Item=N82E16822136742

And what I'd really like to get right now is a Momentus XT Hybrid disk. They're currently $120 for a 500GB model, but it should knock the pants off either disk you posted.

Cache can have a big difference on a drive speed when used for routine or repetitive data transfer. SATA-3 also brings it's advantages. Personally I'd go for the 64MB one if you have backups and all that stuff to make.