There are many differences between Civilization 4 and 5. Besides the obvious graphic changes Some of the most significant game play changes are:
- 1 Military Unit per location, instead of infinite stacks
- Global happiness instead of local happiness
- Embarking troops instead of troop transport units.
An extensive list can be found on the civfanatics forum.
Upcoming expansions might add or remove some of the differences. For example an announced expansion will add religion to Civilization 5, something which was already present in Civilization 4 but absent in the Civilization 5 base game.