I\'m looking for an rsync-like program which will create any missing parent directories on the remote side.
rsync
For example, if I have /top/a/b/c/d
/top/a/b/c/d
i suggest that you enforce the existence manually:
ssh user@remote mkdir -p /top/a/b/c rsync /top/a/b/c/d remote:/top/a/b/c
this creates the target folder if it does not exists already.