I've played with the bug fixer mod since I first got the game, has a lot of changes (most small, but can be significant over the course of a campaign) in it that make more sense then the way it was coded in vanilla versoins. Your not going to be ooheh and awed by it, but its what "vanilla" should have been like in the first place IMHO.
As for mods, I'd recommend Lusted's Terrae Expugnandae mod, I really like the changes and additoins they made in that one the best myself. The SQPR mod was good too, but haven't played it for quite a while so not sure what the latest version is like.
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