To be honest, file system efficiency is the weakest part of Windows. NTFS is just slow when it comes to copying or moving files. The theoretical limits of all hardware connections are never reached. Consider SATA, which is theoretically 3 Gbits/s or nowadays even 6 Gbits/s. Have you ever seen anything like this in real-time file copy? I bet you did not. How about your physical hard drive limitations? Well, a typical Samsung (according to Tom's Hardware HDD charts
) has an average write speed of 110 MB/s. Have you seen anything like that - I have not.
Try to copy a large file between different partitions or different hard drives - the speed is usually way less than that. But - and this is what I think is a big Windows problem - try to copy a large number of small files and your average speed will drop down to 1 MB/s if your lucky. Maybe robocopy helps a bit, I don't use it myself.
I think it's well agreed on that NTFS is not the most efficient file system (ext3 and ext4 are way better). Every time new version of Windows comes out we're promised some new file system, but my Windows 8 consumer preview did not offer me anything better, it formatted the drive at install ... and it's still NTFS.
So, to answer the OP question, basically there is not much you can do. If you have a lot of small files, then it may be worth first combining them into an archive (and maybe compressing after that) and then copying the single archive, but if your folders are not that big, there won't be a whole lot of advantage either.