If you're talking about the Doom mods, the only way to combine them would be to remake them. That's because there isn't a program that combines mods together, and there will be all kinds of overlapping parts in the insides of each mod that will need to be worked around.
To be honest, someone who's comfortable with modding could remake the three mods in one in less than a week, because even though the changes require a good amount of modding skill, it's not a time consuming thing to do if you know what you're doing. I mean, the core of Zerg Doom was done in three days, and then I tweaked it for another four days and had it done in a week.
So, I want to do it, and I know it won't take long, but I've got other priorities like running StarCraft.org which is more important.
QUOTE
Unless He Made Old CWAD Mods.... But Those are for Patch 1.07.
I'm not sure how that works... MPQs and CWADs just store files, they don't quite relate to the ability to combine mods together.