Let's say you have two addons - "ThisAddon" and "ThatAddon" - and you want to combine them into one - "ComboMod".
First, make your "ComboMod" folder and create a "ComboMod.toc" file inside. Now open the .toc file from "ThisAddon" and see what files it's calling. It might look something like:
Code:
## Interface: 20100
## Title: ThisAddon
## Notes: This addon does something.
## Author: Someone
Localization.lua
ThisFile.lua
OtherFile.lua
The part you're interested in are the three lines at the bottom, the actual files it's calling. Copy those lines and paste them at the end of your "ComboMod.toc". Do the same thing with the .toc from "ThatAddon".
If either "ThisAddon" or "ThatAddon" has a dependency (## Dependency: AnotherAddon) listed in its .toc, you'll need to add that to your combo .toc as well.
Then, just copy all of the files from "ThisAddon" and "ThatAddon" - everything but the .toc - into your "ComboMod" folder. If two files have the same name, you'll need to rename one, and remember to change the reference in the .toc.
Another thing to mention is that if you're combining other people's addons, you should just use the result for yourself, and not release it as a new addon. Some addons, like zHunterMod, may appear to combine other mods, but (hopefully) they're either combining two addons by the same author, released by that author as a combo, or they're combining the features of two addons without using the same code as the originals.