If you wanted to allow for converting node modules that use __dirname and __filename, you could adapt those in the define function that is added by using this (what I use for the r.js converter):
var preamble = 'var __filename = module.uri || "", ' +
'__dirname = __filename.substring(0, __filename.lastIndexOf("/") + 1); '
I only do this if I detect __dirname or __filename.
Right yeah, this is a pretty cool feature. I'll leave this open until someone actually has a use case for this in a project though... as of now amd-wrap exists only for Q, which doesn't need it.