I found I could rename include files by specifying a full file name for the target.
For example (nuspec snippet):
<files>
<file src="my-library.js" target="content/my-library.$VERSION$.js">
</files>
and nuget would be run like:
nuget.exe pack mypackage.nuspec -Prop VERSION=1.34
Note: The File extension in src and target must match or the specified target will be treated like a directory.