Mods dont tend to work well together unless designed to from the outset, Generally the mods that are made are story/setting type mods with any changes to retail there to help everything work as the designer expected so they dont tend to work together.
mods that do tend to work chained are
* the MediaVps (yes they are a mod).
* Fury released a branch of the work he did for the BP AI which would work in many situations that use the default AI classes but that is a few years old now iirc and a little tricky to find.
* There have been a few attempts to "fix" the table files for FS2 but they tend to fizzle very quickly and have very unpredictable effects on gameplay and mission balance
but in general its all story/setting related stuff that gets released. usually Mods that work together are released by the same person/team or a fan of that work to create additional campaigns
