Mod Merging
There is currently no tool available for easily merging Skyrim mods. No tool that works as quickly, easily, and effectively as TES4Gecko does for Oblivion. Hopefully a programmer will write a utility for merging Skyrim mods at some point.
Options:
Manually merge in the CK.
Open up two or more mods in the CK at the same time, with the file you want to merge the data to being the active file. Select an item you want to copy and give it a new name. When asked if you want to create a new object, say yes. Be sure to copy every little detail that you want to merge. Let's say you want to merge your NPC into another mod. You may not be able to just copy the actor object into the other mod and get away with it. Your actor might arrive naked, confused, broken, and helpless. If your actor has custom armor, custom AI packages, custom dialog in a custom quest, carries a custom sword, and belongs to a custom faction, you better copy all of those objects into your mod too.
This merging approach is rather time-consuming.
The section on TESVSnip has been removed - the utility is NOT safe to use on your mod at ANY time for anything other than read-only lookups of data. DO NOT USE IT to save data you intend to keep in a live project.
See this topic and this one at Bethesda forums.
If you are working on a modding project with multiple modders and your mod is very complex and does not merge easily using the existing methods, you may consider taking turns working on the file. One modder at a time would work on it while the others would refrain from working on it since anything they built would be very hard to merge in. Alternately, you may figure out what types of work you are doing that are easy to merge. One modder at a time would work on the main file with all of its difficult-to-merge content, and the other modders would build pieces of the mod that you had proven were easy to merge to the main file.