How to limit disk usage (Write/I/O) by application? (NOT space usage)

In Process Explorer, in addition to the regular Normal 8, Below normal 6, Idle 4 priority level, there is an additional Background 4 level, which says that it has Low I/O and Memory Priority. Background 4 results in Very Low I/O priority, according to the corresponding column. That should accomplish what you want.

I believe it is available in Vista and above, as Wikipedia suggests that I/O prioritization was added then.

From your comment it looks like you also want to do this from the command line. I'm not sure if that is available in Process Explorer, but PsTools might have something useful in this regard. I know PsExec lets you launch processes with low priority. If not, it shouldn't be too difficult to whip up a command line program or script to set the priority of a running process.