It's a pretty good rule of thumb that any total conversion mod will conflict with all other total conversion mods. Besdies CCTP I can only think (off the top of my head) of Civilzation Nights (Knights ?) but I think that one was specific to the Vanilla (original version) of the game and is not usable for Gods & Kings or Brave New World.
Any mod that says it uses a modified DLL will automatically be in conflict with all other such mods because there can be only one modded DLL used at one time.
Other rule of thumb is that (as Gilgamesch mentioned) mods whch are changing the same in-game mechanic (or writing to the same game "rule") will nearly always be in conflict with one another. So if two different mods make changes to the tech tree, they are likely to conflict with one another. If two different mods re-work the social policy system, again, conflict.
Sometimes it is more subtle. At one time there were two different world wonder mods where the mod-authors had chosen to give thier world wonder an XML name of BUILDING_TEMPLE_SOLOMAN, or something very near to that. Point is both wonder mods were using the exact same name in the XML, so it was pot-luck which mod was in control of this "thing" the game saw as BUILDING_TEMPLE_SOLOMAN once all mods were loaded. And by pot-luck I mean some players would get Mod 1 loaded before Mod 2, and other players the other way around. Since the game really really hates repeats of code, it would tend to discard nearly everything from whichever mod loaded last. And to make it more funs for players, "nearly everything" is not the same as "everything".