Tutorial (WIP): How Do I Make A PK3 (but is really "What Actually Goes Into A “Map”?)
http://planetwolfenstein.com/4newbies/pakscape.htm
This started out as a tutorial about how to make a PK3 file. However, the real question is “what do you need to put into your PK3?”. The mechanics of actually making the PK3 are very simple. …
I’m sure I missed a bunch of stuff. As always, comments and suggestions are always considered carefully before they are discarded 
You could probably dump all of your custom graphics, sounds, and models into one large folder, but the convention is to seperate them into their respective folders
actually, many things must be in the correct folder.
In many cases, .md3 models and .ase models do not have to be included in the .pk3, because they get cooked into the .bsp at compile time.
It might also be worth mentioning that you should not include a .campaign file in your .pk3 (because players will be required to download it even if it is not in rotation)
As an example, if you look at my textures folder, I have 4 subfolders for all of my custom textures.
- dubrovnik. Textures from a map named Dubrovnik
- egyptsoc_floor. Textures from an Egyptian set by Sock
- iffy. Textures created by me. Notice that anything created by me goes into a subfolder called ‘iffy’
- sub_art. Framed paintings by Subverse
I suggest you do not do this. Instead put them all under
textures/yourmapname
Otherwise, suppose that you use a texture from egyptsoc_floor without a shader. Some other map uses the same texture, under the same name, but also includes a shader with the same name. Suddenly, one of your maps breaks the other. It is much simpler to just keep everything under a unique name.
Shaderlist.txt should never be included. It´s only used by radiant during the compile.
Why it shouldnt be included is that when radiant loads it load all the contents from all pk3´s and takes the shaderlist.txt from the pk3 with the last alphabetic character. So if you have a pak0.pk3 and a zap.pk3 it would load the shaderlist from the zap.pk3 and this would make your shaderlist.txt not being used and could cause alot of trouble to mappers having more than the original pk3 files in their /etmain.
Updated with new pics reflecting the comments above. Also added a section at the end called “common mistakes”.
If there are other common mistakes, regarding PK3 files, that you see people making, let me know what they are, tell me why it’s a bad thing and I’ll add them.