Civilization IV runs in Gambryo. Yes, the Bethesda engine. While this allows a lot of versatility, it also comes with absurd limitations and
an absurd amount of technical debt. I feel that the game would fare better in an engine that doesn't have hooks for physics checks or whatever; I somehow doubt those are going to assist in calculating a simple trade economy.
Interstate 76 was based on the Mechwarrior 2 engine. Cars are not mechs. While it's an incredible game that embraced the lowpoly look, it's also a nightmare to run and deal with. Plus the draw distance is crushingly low. A reimplimentation might be possible, if not for black box voodoo code.
Treasure Adventure Game is full of charm, but controls like a broken ankle and is built on something that was basically an advanced Flash engine is my understanding.
The Creatures Series are advanced artificial life & "artificial DNA" games which have a dreamlike atmosphere and delightful creatures to raise. They also run about as well as banging rocks together; you can; but there are better ways to do so and it's going to take a lot of work to do so. Certainly, OpenC2E exists, but it's also a resurrection of a project that last breathed over a decade ago.
Close Combat: Relying on the Windows Registry instead of simple resource configuration files was a mistake. But that's what you get when publishing under Microsoft. This one stupid issue prevents the games from running on modern "alternate" systems.
System Shock: While the Sekhmet engine does help it run in modern environments, the game
does still control like a computer workstation on wheels. And there's really so much that can be done to fix that while still calling is System Shock 1.
X-Com Apocalypse: Much like Interstate 76 or Creatures, it runs off an old engine that in this case, is a hybrid hellengine. While OpenApoc exists, it's in a pre-alpha state. And sure, running it in Dosbox is definitely an option, but it's a game that wasn't made for that.