Personally I have no interest in having every single hack mod bad dump ect ect
But sorting manual roms manually is not needed
Rom auditing tools like clrmamepro and Romcenter are a must though best for no-intro sets that cover all the official games and mostly just contain good rom dumps
clrmamepro is a more accurate audit tool but Romcenter is more user friendly and can even be used as a front end
If I was going to go down that road again I would still use clrmamepro as the audit tool and Romcenter to look through the roms apply filters ect ect to find what I was looking for while still keeping a full set of games, this even comes in handy if you use flash kits and just direct romcenter to 7-zip instead of an emulator
I'm not 100% sure if those support good tools or not it's been a while but was sure one or both did though or had dat files based on good tool rom sets, it's been even longer since I delved into good sets.