I put all the "orphan" ones in with the original game boxes they correspond to and keep the rest as extras in the original zip locking baggies they came in. The only exceptions being World Championship Baseball, which is in my copy alongside the original overlays, and the Chess/Backgammon/Checkers sets which I keep with my Triple Challenge. My thinking is since these were released by the current rights holders for Intellivision, they count as an official release and should be kept with their actual games. Sort of like an update set in baseball/football card releases.
Interesting organization idea. You don't keep them seperate as part of their original set, but used them to go along with prior 'official release' games. 30 years too late, but still official.