Here is a collection of bugs/oddities collected during various 1.95 games.
General gameplay issues:
If a unit or stack stumbles upon the square an enemy sapper is sitting invisible, the unit(s) get thrown back one square during the sapper's move.
The concept of a spy-sapper unit is not a good one anyway in my opinion, since its only useful for exploring rival territory (or exploiting the bug explained above). I vote to remove it.
The alliances tech does not work, its not possible to offer defensive pacts at all, even if both civs have it.
Increasing the caravan house gold to three seems to be too powerful; its now possible to have research/culture at 100% and still make profit, especially with colossus and great lighthouse.
For the same reason i suggest to decrease the effect of vice royality civic, decreasing distance maintenance by 75% seems to be enough, otherwise the public court is useless in the late game.
I suggest either to remove the artist from garden or one of the theatre ones, otherwise your automated cities produce more artists than everything else. Especially on huge maps its tiresome to manually manage your cities, especially in mid to late game.
Fire catapults are way too powerful! I suggest to triple or even quadruple the building costs and double the costs of normal catapults, and/or reduce the combat stats. (Example: fire catapult: Strength 4, +50% city attack, 80% withdrawal, -50% vs. archery units)
Map:
The fertile crescent map (huge) should have some ocean between europe and northern africa, otherwise that area spawns so many barbarian biremes which makes it impossible for any AI nation to build up naval force in the early game (with the exception of greece).
Otherwise, i want to state that your mod is the only reason for me to play civ4 now and then! Keep up the good work!