Basic situation:
I am copying some NTFS disks in openSuSE. Each one is 2TB. When I do this, the system runs slow.
My guesses:
Kristof Provost was very close, but in my situation, I didn't want to use dd or write my own software, so the solution was to use the "--drop-cache" option in rsync.
I have used this many times since creating this question, and it seems to fix the problem completely. One exception was when I am using rsync to copy from a FreeBSD machine, which doesn't support "--drop-cache". So I wrote a wrapper to replace the /usr/local/bin/rsync command, and remove that option, and now it works copying from there too.
It still uses huge amount of memory for buffers, and seems to keep almost no cache, but works smoothly anyway.
$ free
total used free shared buffers cached
Mem: 24731544 24531576 199968 0 15349680 850624
-/+ buffers/cache: 8331272 16400272
Swap: 4194300 602648 3591652