I’m going through all my sets since 1 year and check every single game, keeping only my favorites, does not only shrink down the collection, but also saves you from having several Barbie & Co. stuff in your setup. That takes a lot of time, but it’s absolutely worth the time spent. Of course that is what I personally do now, a lot of people want to keep every single game from the set, but that ship has sailed for me.
I also did a favorite MAME set a while ago and it was absolutely worth it. Lately I was going through the TOSEC of C64, and it took me around 2 months to go through, and I ended up with around 2.000 games still, absolutely no need to keep it all, there’s a lot of trash on the C64. With the Amiga it was different as in my opinion the Amiga almost only has good games.
The last thing I did some weeks ago, was going through all of the fan translations of several consoles and there are quite some of them. But having some great RPGs translated that never came out in English language is just awesome.
One last thing is that having these personal “clean” sets is that I can now use them anywhere I want without doing it again. I use several handhelds with emulation, and Raspberry Pi and stuff, and I can just use my ready sets without having to start over.