Multimod and you, or more correctly, me

[Suicide Junkie]

There are only a few mods which work together, and don't change the same files.
There is no program to merge mods, and even humans would have a very tough time with it.

Now, for the big name mods that do work well with others:
- FQM standard (generate the map, then load the map for play in almost any other mod)
- TDM (Changes AIs, not datafiles, plus adds some strategies and formations) Works with mods that don't change the base files too much.
- Single-file mods (usually named after the file they change) usually fits adequately after some copy & paste or tweaking.

Pirates & Nomads has extensive changes, but I have written an AI Patcher program to tweak TDM and other standard SE4 AIs into P&N-usable form.
Look for it in the P&N download section.

Other modders will surely chime in now