Romcenter - Romcenter is a GUI driven tool for curating ROM sets. It allows you to load in XML dat files and rebuild your collection into your preferred romset structure. It is a little simpler to get started with than clrmamepro
clrmamepro - clrmamepro is the standard tool for managing ROM sets. It is very powerful, but also a bit hard to get started with
JRomManager - A rom manager written entirely in Java. Can be used on OSX and Linux
ROMLister - ROMLister is a tool to filter ROM sets based on a wide variety of ROM metadata