Done this recently with my Mame selection. I personally went with 650 roms including all the games from a good franchise or series, like KoF, Street Fighter, 1945 etc etc. I didn't really concentrate too much on the classic 70s and early 80s games because I didn't think they'd get played. Pac-man, Defender, Robotron and any actual good classics are in there, I'm picky but not a monster.
I trawled through a merged set, manually gathering all the roms I needed for others after I selected the ones I wanted. Even going as far as opening the zips up and adding the bins they needed to run, and re-zipping.
I spent 2 weeks doing this including testing, gathering bios files, and config for certain roms.
To find this project going on and realising I should have used a non-merged set, and just how much time I could have saved made me want to cry. But I learnt a hell of a lot about Mame...kinda. I should have stayed in school.
For what its worth do you want to see the list of titles I went with?