My friend and I live "across the tracks" in game history: his was Quake and Duke Nukem, and mine was Half-Life and Team Fortress. I got sick and tired of all the serious games, and wanted something a bit more (1) humorous and (2) run around and frag things.
Therefore my friend recommended Duke Nukem 3D (I play it with eduke32 and high res pack)... which I have now played and love.
Now that I've played it, however, I want to mod it. I've seen a few sites that give you step by steps for single bits, like "make a map" or "add a sound effect." (Although I haven't found "replace a texture" yet).
However, I haven't found anything that ties it all together. Like making a total conversion. I want to change the title screen, change the menu screens, change the text in game, replace the standard gun art with custom gun art, change the enemy sprites to new sprites, change the music to new music, the whole shishkebab.
I've even got a game document :D
It looks like a "mod" for Duke Nukem is basically a subdirectory with game content directories or a GRP file that archives all the game content, and then with eduke32 I can point it to the new game directory.
Is this right? Does anyone have some good pointers on the "whole shishkebab" front? How do you go about changing all the little bits that make Duke Duke (assuming you've got a plan and some local art, like I do)? How do you add a new type of gun? CAN you add a new type of gun?
I've got this idea, but I don't know where to even start :D Except get another can of Dr Pepper and just play more Duke instead!

It hasn't been this way until recently when EDuke32 was updated to allow it.
There is no way of adding new guns in vanilla Duke Nukem 3D (1.3D or 1.5, which is available here at GOG). In past, modders always had to "replace" the current selection weapons by rewriting their specifications, even this was very limited until EDuke was introduced.
Pretty much anything is possible with EDuke32 -- if it's not, there's a high change it will be made possible if you just talk to the people who are developing it.
There is quite a big mod community for Duke3D and you should find some easily over ar the Duke4.net forums, no matter how big or small the question is.
I can't go into details here since it would require alot of lines of code and alot of explaining for a new modder, but I suggest you take a look at the .CON files, which have a good portion of the game's "code" (CON is a scripting system with a syntax similar to C).
- USER.CON holds the values for weapons and items, plus other things such as how many times the freezeblast bounces of walls.
- GAME.CON holds the actual AI routines for monsters and how in-game objects work: such item pickups and what effects are called when you pick them up.
- DEFS.CON holds all the names for the variables, it's loaded first so
These are are regular text files which can be opened with Notepad.
For things like adding completely new weaponry you need to know new EDuke32 commands and functions which are nicely listed on the [url=http://wiki.eduke32.com/wiki/Category:All_commands]EDuke32 wiki[/url].
For beginners, try to find the values for each weapons in the USER.CON, for examples of actual code, see GAME.CON and the MYENEMY actor which should be right at the top of the file, the developers had commented all the lines, telling what each of them do.