A few additions:
In addition to the issues already on the list, we've had no updates since July 2017. The missing updates cover a variety of bug fixes plus new languages (Turkish, Danish). Current GOG v1.4.030r, current Steam v1.4.035r.
Meridian: New World
Sad case here. We're missing the final v1.05 update for the game. The dev *wants* to provide it, but due to the DRM in his now-unsupported game engine, he's unable to create the required GOG build. There's definitely a cautionary tale in there. :-( The missing update mostly addresses performance issues.
Source (see comments) : https://steamcommunity.com/app/265120/discussions/0/357286663690878984/?ctp=2
Guild Of Dungeoneering
GOG is missing the last two updates (both released in 2017). These include numerous fixes, plus a new Trophy Trial game mode. Current GOG v1.09, current Steam v1.11.
Missing all updates since Feb 2018. This includes lots of bug fixes, plus a newly-added minimap. Current GOG v1.1.71, current Steam v1.1.101.