Huge fan of City-State Diplomacy Mod, because it requires you to build diplomatic units and send them to City-States, while also removing mini-quests like eliminating rival City States. The latter kind of blows up late games in vanilla, because the AI will often go nuts and conquer neighboring CS's anyway.
I like Balance - Terrain Improvements a great deal, specifically for the ability to improve luxury and strategic resources with great people. In vanilla, I often avoid tile improvements with GP's mid-game, for fear of building an academy, merchant house, or monument on a late appearing strategic resource. While this mod doesn't alleviate the risk of placing an academy on a future oil tile, it makes for interesting uses for GP's. (Engineers on mines, quarries; merchants on sugar; artists on gold, etc)
Balance - Social Policies is also a personal favorite, as it gives you a free policy each era, along with tweaking some of the 2nd or 3rd tier early policies, making them an interesting choice. Haven't played a game, post-patch with this one, so I might not enjoy it as much as I did in the past. Still, a mod that grants a free policy each era is a very, very good addition to the game.
I'm looking at Food Economy MOD closely. I want to try it next game.