phaolo: Users could report them, like we do now.
(an automatic notification system would be better, however) How exactly would you automate it, ie. how could the system check automatically from all the other stores whether the GOG version is out of date, and whether there are important updates (missing)?
Even if it was semi-automated (somehow trying to decipher the version number on the Steam version, and checking it against the GOG version number, for example), there would still be lots of manual cross-checking involved.
I think the current way is quite good: vigilant GOGers find them out, inform GOG, and then it is up to GOG to try to push the update to GOG. And at the same time, the GOGers keep a list of such outdated games, as a buyer's beware list (this can also be considered as such a way of communication from GOG users to the GOG staff).