Whichever is cheaper (I guess eSATA). There's no way you can reach eSATA's limit of 300MB/s and if USB 2.0 is any indication, you won't be getting more than 50% of supposed speed from USB 3.0 (which is beyond reach of most hdds too).

You should also be aware that eSATA takes less processor time.

 

My preference would be for eSATA. This isn't based on a great deal of knowledge about either, but I would expect eSATA to be more mature (USB 3 is what, a few months old?). Also, while USB 3 has some huge theoretical throughput, in practice USB 2 never came close to its maximum; I imagine it's fundamentally pretty similar so would also not expect it to reach anywhere near the published numbers. Should still be enough to max out a hard drive, admittedly.

 

eSATA. By a long shot.

The only benefit USB3 has over it in your circumstance is that it will provide power so you could buy a bus powered USB3 external hard drive. If you want speed, an eSATA external hard drive or HDD enclosure will provide speeds as if it were a normal HDD plugged in like normal to the SATA port. Thats all eSATA is, a sata port with a different connector. Meaning with a externally powered external HDD that has eSATA it will be very fast.

 

If you're planning on only connecting it to your laptop, I would probably pick eSATA. However, if you want it to be more portable and usable on other computers, go with the USB 3.0 (it's backwards compatible with USB 2.0).

It also depends on what size you get. The WD MyBook (USB 3.0) has similar throughput speeds to an eSATA device, but is pretty large. Smaller USB 3.0 devices tend to be slower (some not much faster than USB 2.0). Currently, the biggest problem with USB 3.0 is that it's spotty. Some devices are excellent, and others are complete crap. eSATA is a pretty maure technology now, so the differences between devices are going to be less extreme.

Prices aren't too much different ($120 for a WD 1TB eSATA, $140 for the USB 3.0 version on Newegg), so it really comes down to a matter of personal preference.

*Edit* You can also read this article.

 

This. I believe I mentioned quite a long time ago that I setup an eSata based harddrive array. Essentially I have a 10 TB HDD array setup in a raid 1 format, that ultimately connects to a dual core desktop setup on my network as a media server. The array acts just as an internal HDD would. It's been there for about a year now, constantly connected with no issues. Truth be told, You'll never really reach even close to the maximum transfer rate with conventional HDDs, and probably not with SSD's either (though they're so expensive I can't imagine using SSD's for media storage).

 

They have already maxed out SATA II's capabilities with SSD. SSD's are insanely fast compared to normal HDD's. They have yet to defeat the next SATA standard, SATA III, as far as I know.

For speed, SSD's are king, use them for OS drives and for applications requiring fast hard drive access and write speeds. Use normal HDD's for storage.