I have clrmame dump any disks to a temp directory called NEW. From there, I move the files to where I want them. A good dir util and you won't need a renamer program to place files in their ultimate destination.
Most ftp's I see place their TOSEC files in dirs based on the dats they are housed in, but I had my dir structure before there ever was a TOSEC and I more or less still use the same ones (messy as it may be). I have folders for each letter and inside them are only commercial games; if I am unsure of a game's commercial status, I just leave them with the commercial stuff. PD games have their own area. For me, it is important to designate that division, your mileage may vary.
I know I have an ultimate vision of all the files being in this panacea of dir structures which will probably never happen, but I try to keep it all somewhat navigable.