For a while I tried to have every version, but it just became unmanageable to my standards so I ended up trying to find the best version of each game. There is something satisfying when the total number of games for a platform in Launchbox matches the amount of files in the folder (aside from multi-discs of course). I usually go with whatever version Retroachievements supports. I will keep a duplicate of a game as a seperate entry if it has some interesting or significant difference like with Contra/Probotector.
I only really keep prototypes or unreleased games if they are particularly interesting. On the other hand, I want just about any decent ROM hack or homebrew game. I got way into Game Boy homebrew recently.