I loved the first versions of Civilization and Masters of Orion. I tried one of the more recent version of Civilization and didn't like it anything like as much. But I am a lot older - so it could just be me. How do more recent versions of Masters of Orion hold up?
Moo2 is good. Moo1 avoided a lot of the city micromanagement that civilization had. Moo2 is a hybrid of moo1 in civilization.
Moo3 I never played, mostly based on the recommendations and reviews of other moo players.
I played civilization through civilization 3, and I muck around a lot with free civ, which is kind of hackable.
There's also remnants of the precursors, a Java remake of mu1 that I found very hackable. I've been able to run it from IntelliJ and hacked the source code.